Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:54:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/04_2023/6x13_21987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/04_2023/6x13_21987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/04_2023/6x13_21987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/04_2023/6x13_21987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/04_2023/6x13_21987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x13_21987/04_2023/6x13_21987_updated.pdb" } resolution = 3.66 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= 0.003 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 P 1 5.49 5 S 18 5.16 5 C 2067 2.51 5 N 501 2.21 5 O 549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3136 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3136 Unusual residues: {'6OU': 1} Classifications: {'peptide': 417, 'undetermined': 1} Link IDs: {'PTRANS': 18, 'TRANS': 398, None: 1} Not linked: pdbres="THR A 418 " pdbres="6OU A 501 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.21, per 1000 atoms: 0.70 Number of scatterers: 3136 At special positions: 0 Unit cell: (66.5415, 78.3473, 71.9078, 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 18 16.00 P 1 15.00 O 549 8.00 N 501 7.00 C 2067 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: 1.29 Conformation dependent library (CDL) restraints added in 563.9 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 37 through 71 removed outlier: 3.767A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.340A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.929A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 106 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.213A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 219 removed outlier: 3.850A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.771A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 253 Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 296 through 308 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 377 through 417 removed outlier: 3.754A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 687 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: 0.82 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 482 1.31 - 1.43: 788 1.43 - 1.56: 1878 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3196 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.562 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.580 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3191 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.67: 95 106.67 - 113.29: 1814 113.29 - 119.91: 1066 119.91 - 126.53: 1344 126.53 - 133.15: 30 Bond angle restraints: 4349 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.38 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.46 -10.65 2.21e+00 2.05e-01 2.32e+01 angle pdb=" N GLY A 357 " pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.34e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C THR A 275 " pdb=" N ARG A 276 " pdb=" CA ARG A 276 " ideal model delta sigma weight residual 122.08 127.30 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 4344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 1765 25.76 - 51.51: 97 51.51 - 77.27: 13 77.27 - 103.03: 1 103.03 - 128.78: 2 Dihedral angle restraints: 1878 sinusoidal: 696 harmonic: 1182 Sorted by residual: dihedral pdb=" CA LEU A 372 " pdb=" C LEU A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C09 6OU A 501 " pdb=" C10 6OU A 501 " pdb=" C11 6OU A 501 " pdb=" C12 6OU A 501 " ideal model delta sinusoidal sigma weight residual 179.71 -51.51 -128.78 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C20 6OU A 501 " pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " pdb=" C33 6OU A 501 " ideal model delta sinusoidal sigma weight residual -177.41 -63.97 -113.44 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 1875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 347 0.040 - 0.080: 138 0.080 - 0.119: 43 0.119 - 0.159: 7 0.159 - 0.199: 5 Chirality restraints: 540 Sorted by residual: chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA LEU A 303 " pdb=" N LEU A 303 " pdb=" C LEU A 303 " pdb=" CB LEU A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 537 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 45 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 243 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ILE A 243 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 243 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 244 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 303 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 304 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.031 5.00e-02 4.00e+02 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1024 2.85 - 3.36: 3094 3.36 - 3.88: 5142 3.88 - 4.39: 5510 4.39 - 4.90: 9835 Nonbonded interactions: 24605 Sorted by model distance: nonbonded pdb=" O LYS A 414 " pdb=" OG1 THR A 418 " model vdw 2.340 2.440 nonbonded pdb=" OD1 ASP A 390 " pdb=" NH1 ARG A 397 " model vdw 2.402 2.520 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.438 2.440 nonbonded pdb=" NZ LYS A 196 " pdb=" O24 6OU A 501 " model vdw 2.439 2.520 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 177 " model vdw 2.454 2.520 ... (remaining 24600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 3.590 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.007 0.086 3196 Z= 0.413 Angle : 1.044 15.434 4349 Z= 0.516 Chirality : 0.048 0.199 540 Planarity : 0.008 0.065 533 Dihedral : 16.269 128.781 1130 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.27 % 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: -3.73 (0.31), residues: 415 helix: -2.04 (0.20), residues: 351 sheet: None (None), residues: 0 loop : -3.62 (0.61), residues: 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.345 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1612 time to fit residues: 12.0231 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3196 Z= 0.220 Angle : 0.610 6.727 4349 Z= 0.313 Chirality : 0.038 0.119 540 Planarity : 0.006 0.069 533 Dihedral : 10.577 97.984 470 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.92 % 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: -0.97 (0.39), residues: 415 helix: 0.04 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -3.96 (0.55), residues: 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.353 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1479 time to fit residues: 10.8916 Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0357 time to fit residues: 0.6004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3196 Z= 0.275 Angle : 0.635 6.415 4349 Z= 0.325 Chirality : 0.040 0.122 540 Planarity : 0.005 0.072 533 Dihedral : 9.425 94.234 470 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 1.23 % 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: 0.03 (0.41), residues: 415 helix: 0.71 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -3.63 (0.59), residues: 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.318 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.1477 time to fit residues: 10.1670 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0319 time to fit residues: 0.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3196 Z= 0.185 Angle : 0.580 6.306 4349 Z= 0.294 Chirality : 0.038 0.127 540 Planarity : 0.005 0.076 533 Dihedral : 8.169 84.990 470 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 2.15 % 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: 0.69 (0.42), residues: 415 helix: 1.19 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.46 (0.59), residues: 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.372 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.1412 time to fit residues: 10.8306 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0386 time to fit residues: 0.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3196 Z= 0.251 Angle : 0.610 6.332 4349 Z= 0.313 Chirality : 0.039 0.135 540 Planarity : 0.005 0.079 533 Dihedral : 7.917 84.117 470 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 1.85 % 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: 0.85 (0.42), residues: 415 helix: 1.29 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -3.34 (0.61), residues: 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.345 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.1488 time to fit residues: 10.5631 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0351 time to fit residues: 0.5891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3196 Z= 0.236 Angle : 0.612 7.225 4349 Z= 0.311 Chirality : 0.039 0.147 540 Planarity : 0.005 0.082 533 Dihedral : 7.778 82.043 470 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.62 % 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: 1.03 (0.42), residues: 415 helix: 1.41 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.21 (0.62), residues: 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.377 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.1541 time to fit residues: 10.0484 Evaluate side-chains 49 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0360 time to fit residues: 0.5105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8154 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.245 Angle : 0.615 6.411 4349 Z= 0.313 Chirality : 0.040 0.169 540 Planarity : 0.005 0.083 533 Dihedral : 7.672 79.751 470 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.92 % 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: 1.05 (0.42), residues: 415 helix: 1.43 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -3.23 (0.63), residues: 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.344 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1489 time to fit residues: 9.8433 Evaluate side-chains 49 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0343 time to fit residues: 0.5975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.0040 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3196 Z= 0.206 Angle : 0.594 6.799 4349 Z= 0.302 Chirality : 0.039 0.159 540 Planarity : 0.005 0.083 533 Dihedral : 7.418 74.239 470 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.62 % 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: 1.26 (0.42), residues: 415 helix: 1.57 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -3.12 (0.63), residues: 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.351 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.1669 time to fit residues: 10.6500 Evaluate side-chains 46 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0345 time to fit residues: 0.5421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.256 Angle : 0.632 8.700 4349 Z= 0.320 Chirality : 0.039 0.165 540 Planarity : 0.005 0.084 533 Dihedral : 7.451 73.863 470 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: 1.27 (0.42), residues: 415 helix: 1.57 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1574 time to fit residues: 9.3958 Evaluate side-chains 46 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8135 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3196 Z= 0.228 Angle : 0.646 10.221 4349 Z= 0.320 Chirality : 0.039 0.173 540 Planarity : 0.005 0.084 533 Dihedral : 7.346 70.800 470 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.31 % 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: 1.28 (0.42), residues: 415 helix: 1.56 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -2.96 (0.65), residues: 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.284 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1642 time to fit residues: 9.7477 Evaluate side-chains 48 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0313 time to fit residues: 0.4756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099702 restraints weight = 4260.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102064 restraints weight = 2858.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103855 restraints weight = 2211.748| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3196 Z= 0.206 Angle : 0.623 8.721 4349 Z= 0.310 Chirality : 0.039 0.171 540 Planarity : 0.005 0.078 533 Dihedral : 6.755 63.088 470 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.00 % 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: 1.35 (0.43), residues: 415 helix: 1.59 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -2.82 (0.68), residues: 68 =============================================================================== Job complete usr+sys time: 966.84 seconds wall clock time: 17 minutes 56.41 seconds (1076.41 seconds total)