Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:53:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/11_2022/8csv_26972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/11_2022/8csv_26972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/11_2022/8csv_26972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/11_2022/8csv_26972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/11_2022/8csv_26972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csv_26972/11_2022/8csv_26972.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.227 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "W TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3712 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3431 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} 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: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 233 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Time building chain proxies: 3.94, per 1000 atoms: 1.06 Number of scatterers: 3712 At special positions: 0 Unit cell: (92.13, 110.39, 60.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 734 8.00 N 677 7.00 C 2286 6.00 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: 1.55 Conformation dependent library (CDL) restraints added in 714.3 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 65.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 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 removed outlier: 3.541A pdb=" N GLU A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 146 through 154 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 229 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.545A pdb=" N ASN A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) 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 447 Processing helix chain 'A' and resid 449 through 460 removed outlier: 3.596A pdb=" N LYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) 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 22 190 hydrogen bonds defined for protein. 561 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: 0.99 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1285 1.34 - 1.46: 646 1.46 - 1.58: 1770 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3726 Sorted by residual: bond pdb=" C LEU A 417 " pdb=" N PRO A 418 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.27e-01 bond pdb=" CA VAL A 437 " pdb=" CB VAL A 437 " ideal model delta sigma weight residual 1.540 1.550 -0.009 1.36e-02 5.41e+03 4.87e-01 bond pdb=" C ASP W 25 " pdb=" N ILE W 26 " ideal model delta sigma weight residual 1.330 1.325 0.005 8.40e-03 1.42e+04 3.42e-01 bond pdb=" CA LEU A 417 " pdb=" C LEU A 417 " ideal model delta sigma weight residual 1.520 1.527 -0.007 1.23e-02 6.61e+03 3.41e-01 bond pdb=" N PRO W 24 " pdb=" CA PRO W 24 " ideal model delta sigma weight residual 1.469 1.476 -0.007 1.28e-02 6.10e+03 3.40e-01 ... (remaining 3721 not shown) Histogram of bond angle deviations from ideal: 100.25 - 106.46: 117 106.46 - 112.68: 2031 112.68 - 118.89: 1024 118.89 - 125.11: 1840 125.11 - 131.32: 49 Bond angle restraints: 5061 Sorted by residual: angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 113.39 109.15 4.24 1.47e+00 4.63e-01 8.33e+00 angle pdb=" C LYS A 436 " pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 121.97 127.12 -5.15 1.80e+00 3.09e-01 8.17e+00 angle pdb=" CA VAL A 172 " pdb=" C VAL A 172 " pdb=" N ARG A 173 " ideal model delta sigma weight residual 118.55 116.70 1.85 8.60e-01 1.35e+00 4.60e+00 angle pdb=" O ASP A 337 " pdb=" C ASP A 337 " pdb=" N HIS A 338 " ideal model delta sigma weight residual 122.39 124.83 -2.44 1.29e+00 6.01e-01 3.58e+00 angle pdb=" CA VAL A 437 " pdb=" CB VAL A 437 " pdb=" CG1 VAL A 437 " ideal model delta sigma weight residual 110.40 113.35 -2.95 1.70e+00 3.46e-01 3.01e+00 ... (remaining 5056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 2127 17.25 - 34.50: 107 34.50 - 51.76: 25 51.76 - 69.01: 8 69.01 - 86.26: 2 Dihedral angle restraints: 2269 sinusoidal: 876 harmonic: 1393 Sorted by residual: dihedral pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " pdb=" CG ARG A 173 " pdb=" CD ARG A 173 " ideal model delta sinusoidal sigma weight residual -180.00 -121.72 -58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG A 187 " pdb=" CB ARG A 187 " pdb=" CG ARG A 187 " pdb=" CD ARG A 187 " ideal model delta sinusoidal sigma weight residual -180.00 -121.75 -58.25 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " pdb=" CD GLU A 96 " pdb=" OE1 GLU A 96 " ideal model delta sinusoidal sigma weight residual 0.00 83.13 -83.13 1 3.00e+01 1.11e-03 9.39e+00 ... (remaining 2266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 339 0.026 - 0.051: 157 0.051 - 0.077: 75 0.077 - 0.103: 22 0.103 - 0.128: 4 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 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA LEU A 417 " pdb=" N LEU A 417 " pdb=" C LEU A 417 " pdb=" CB LEU A 417 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA PRO A 418 " pdb=" N PRO A 418 " pdb=" C PRO A 418 " pdb=" CB PRO A 418 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 594 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 439 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 440 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 307 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO A 308 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 373 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 374 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.021 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 716 2.78 - 3.31: 3724 3.31 - 3.84: 6586 3.84 - 4.37: 8167 4.37 - 4.90: 12809 Nonbonded interactions: 32002 Sorted by model distance: nonbonded pdb=" O PRO A 364 " pdb=" O HOH A1901 " model vdw 2.246 2.440 nonbonded pdb=" O ASP A 316 " pdb=" O HOH A1902 " model vdw 2.289 2.440 nonbonded pdb=" O LEU A 389 " pdb=" OG1 THR A 393 " model vdw 2.292 2.440 nonbonded pdb=" O VAL A 104 " pdb=" O HOH A1903 " model vdw 2.303 2.440 nonbonded pdb=" O HOH A1939 " pdb=" O HOH A1948 " model vdw 2.316 2.440 ... (remaining 31997 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2286 2.51 5 N 677 2.21 5 O 734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.550 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 18.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3726 Z= 0.152 Angle : 0.467 5.577 5061 Z= 0.263 Chirality : 0.037 0.128 597 Planarity : 0.005 0.045 668 Dihedral : 11.849 86.262 1365 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.37), residues: 479 helix: 0.70 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 0.52 (0.51), residues: 161 *********************** 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 **************************** Evaluate side-chains 88 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.446 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 85 average time/residue: 1.1655 time to fit residues: 102.4250 Evaluate side-chains 59 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1816 time to fit residues: 0.8645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 165 ASN A 237 GLN A 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 3726 Z= 0.136 Angle : 0.442 6.332 5061 Z= 0.229 Chirality : 0.036 0.121 597 Planarity : 0.005 0.036 668 Dihedral : 3.846 13.152 509 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.51 % Favored : 97.29 % Rotamer Outliers : 1.55 % 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: 1.63 (0.38), residues: 479 helix: 1.34 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.77 (0.53), 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 **************************** Evaluate side-chains 68 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.469 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 1.1015 time to fit residues: 73.3397 Evaluate side-chains 57 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0525 time to fit residues: 0.7242 ------------------------------------------------------------------------------- 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: 0.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 38 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN A 215 HIS A 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.013 3726 Z= 0.113 Angle : 0.406 5.858 5061 Z= 0.209 Chirality : 0.035 0.128 597 Planarity : 0.004 0.033 668 Dihedral : 3.610 11.266 509 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer Outliers : 1.55 % 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: 2.08 (0.39), residues: 479 helix: 1.72 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.88 (0.53), 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 **************************** Evaluate side-chains 65 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.471 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 1.0069 time to fit residues: 65.0126 Evaluate side-chains 58 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0934 time to fit residues: 0.8241 ------------------------------------------------------------------------------- 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: 9.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1608 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= 0.155 Angle : 0.438 7.162 5061 Z= 0.224 Chirality : 0.037 0.128 597 Planarity : 0.004 0.034 668 Dihedral : 3.744 14.041 509 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.51 % Favored : 97.29 % Rotamer Outliers : 2.07 % 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: 2.09 (0.38), residues: 479 helix: 1.75 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.83 (0.53), 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 **************************** Evaluate side-chains 64 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.551 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 1.1231 time to fit residues: 70.2673 Evaluate side-chains 61 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0596 time to fit residues: 0.9211 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3726 Z= 0.135 Angle : 0.432 7.924 5061 Z= 0.219 Chirality : 0.036 0.127 597 Planarity : 0.004 0.034 668 Dihedral : 3.650 12.996 509 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer Outliers : 1.29 % 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: 2.25 (0.39), residues: 479 helix: 1.88 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.87 (0.53), 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 **************************** Evaluate side-chains 60 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.490 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 1.0520 time to fit residues: 63.5591 Evaluate side-chains 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0964 time to fit residues: 0.7555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 3726 Z= 0.120 Angle : 0.419 8.424 5061 Z= 0.210 Chirality : 0.035 0.128 597 Planarity : 0.004 0.033 668 Dihedral : 3.546 12.087 509 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer Outliers : 1.81 % 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: 2.39 (0.39), residues: 479 helix: 1.98 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.92 (0.53), 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 **************************** Evaluate side-chains 64 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.457 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 1.0178 time to fit residues: 63.6772 Evaluate side-chains 60 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0873 time to fit residues: 0.9744 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 9 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3726 Z= 0.156 Angle : 0.454 9.117 5061 Z= 0.228 Chirality : 0.036 0.129 597 Planarity : 0.004 0.034 668 Dihedral : 3.663 15.875 509 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.34 % Favored : 96.45 % Rotamer Outliers : 1.03 % 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: 2.37 (0.39), residues: 479 helix: 1.97 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.91 (0.53), 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 **************************** Evaluate side-chains 62 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.485 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 1.0484 time to fit residues: 65.4704 Evaluate side-chains 59 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1228 time to fit residues: 0.9268 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 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 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3726 Z= 0.189 Angle : 0.478 9.855 5061 Z= 0.239 Chirality : 0.038 0.128 597 Planarity : 0.004 0.033 668 Dihedral : 3.813 14.104 509 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer Outliers : 1.55 % 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 (0.38), residues: 479 helix: 1.85 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.81 (0.53), 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 **************************** Evaluate side-chains 62 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.471 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 1.0355 time to fit residues: 63.6109 Evaluate side-chains 57 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1619 time to fit residues: 0.8419 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN A 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3726 Z= 0.164 Angle : 0.473 10.222 5061 Z= 0.235 Chirality : 0.037 0.128 597 Planarity : 0.004 0.033 668 Dihedral : 3.744 13.544 509 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.92 % Favored : 96.87 % Rotamer Outliers : 1.55 % 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: 2.23 (0.38), residues: 479 helix: 1.88 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.83 (0.53), 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 **************************** Evaluate side-chains 62 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.495 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.9992 time to fit residues: 60.5596 Evaluate side-chains 59 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0640 time to fit residues: 0.8230 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 0.0870 chunk 29 optimal weight: 0.0060 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 165 ASN A 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3726 Z= 0.122 Angle : 0.452 10.521 5061 Z= 0.222 Chirality : 0.035 0.130 597 Planarity : 0.004 0.032 668 Dihedral : 3.519 11.689 509 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.34 % Favored : 96.45 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.39), residues: 479 helix: 2.06 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.94 (0.54), 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 **************************** Evaluate side-chains 63 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.463 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 1.0378 time to fit residues: 66.9396 Evaluate side-chains 60 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0367 time to fit residues: 0.6827 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 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 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114058 restraints weight = 3899.986| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.27 r_work: 0.3148 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work: 0.3107 rms_B_bonded: 1.40 restraints_weight: 0.1250 r_work: 0.3079 rms_B_bonded: 1.73 restraints_weight: 0.0625 r_work: 0.3044 rms_B_bonded: 2.21 restraints_weight: 0.0312 r_work: 0.2997 rms_B_bonded: 2.91 restraints_weight: 0.0156 r_work: 0.2932 rms_B_bonded: 3.97 restraints_weight: 0.0078 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3726 Z= 0.207 Angle : 0.501 10.630 5061 Z= 0.250 Chirality : 0.038 0.128 597 Planarity : 0.004 0.032 668 Dihedral : 3.880 14.235 509 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.71 % Favored : 97.08 % Rotamer Outliers : 0.78 % 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: 2.09 (0.38), residues: 479 helix: 1.77 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.76 (0.53), residues: 159 =============================================================================== Job complete usr+sys time: 1879.25 seconds wall clock time: 34 minutes 37.63 seconds (2077.63 seconds total)