Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:08:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkh_14042/11_2022/7qkh_14042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkh_14042/11_2022/7qkh_14042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkh_14042/11_2022/7qkh_14042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkh_14042/11_2022/7qkh_14042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkh_14042/11_2022/7qkh_14042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkh_14042/11_2022/7qkh_14042.pdb" } resolution = 3.17 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= 0.001 sd= 0.004 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 None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3105 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "B" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "D" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Time building chain proxies: 1.81, per 1000 atoms: 0.58 Number of scatterers: 3105 At special positions: 0 Unit cell: (58.16, 139.584, 33.442, 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 6 16.00 O 288 8.00 N 273 7.00 C 945 6.00 H 1593 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 274.7 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AA2, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AA3, first strand: chain 'B' and resid 296 through 297 removed outlier: 6.313A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 305 through 309 removed outlier: 6.260A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.460A pdb=" N LYS G 294 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 298 through 299 removed outlier: 6.582A pdb=" N LYS G 298 " --> pdb=" O HIS E 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.383A pdb=" N VAL G 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 313 through 316 32 hydrogen bonds defined for protein. 96 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: 1.09 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 1586 1.09 - 1.27: 256 1.27 - 1.45: 348 1.45 - 1.63: 924 1.63 - 1.81: 6 Bond restraints: 3120 Sorted by residual: bond pdb=" N ILE A 297 " pdb=" H ILE A 297 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE G 297 " pdb=" H ILE G 297 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS B 298 " pdb=" H LYS B 298 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N HIS D 299 " pdb=" H HIS D 299 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" NE2 GLN B 307 " pdb="HE21 GLN B 307 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3115 not shown) Histogram of bond angle deviations from ideal: 71.99 - 84.67: 21 84.67 - 97.36: 7 97.36 - 110.04: 2876 110.04 - 122.73: 2552 122.73 - 135.41: 235 Bond angle restraints: 5691 Sorted by residual: angle pdb=" CB VAL E 313 " pdb=" CA VAL E 313 " pdb=" HA VAL E 313 " ideal model delta sigma weight residual 109.00 71.99 37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA VAL E 313 " pdb=" CB VAL E 313 " pdb=" HB VAL E 313 " ideal model delta sigma weight residual 109.00 72.93 36.07 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CB VAL G 313 " pdb=" CA VAL G 313 " pdb=" HA VAL G 313 " ideal model delta sigma weight residual 109.00 73.33 35.67 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N VAL E 313 " pdb=" CA VAL E 313 " pdb=" HA VAL E 313 " ideal model delta sigma weight residual 110.00 74.59 35.41 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" HA VAL C 313 " ideal model delta sigma weight residual 110.00 75.23 34.77 3.00e+00 1.11e-01 1.34e+02 ... (remaining 5686 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.34: 997 15.34 - 30.66: 128 30.66 - 45.99: 22 45.99 - 61.32: 25 61.32 - 76.65: 25 Dihedral angle restraints: 1197 sinusoidal: 591 harmonic: 606 Sorted by residual: dihedral pdb=" C VAL C 313 " pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" CB VAL C 313 " ideal model delta harmonic sigma weight residual -122.00 -141.49 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" C VAL G 313 " pdb=" N VAL G 313 " pdb=" CA VAL G 313 " pdb=" CB VAL G 313 " ideal model delta harmonic sigma weight residual -122.00 -139.63 17.63 0 2.50e+00 1.60e-01 4.97e+01 dihedral pdb=" N VAL C 313 " pdb=" C VAL C 313 " pdb=" CA VAL C 313 " pdb=" CB VAL C 313 " ideal model delta harmonic sigma weight residual 123.40 140.78 -17.38 0 2.50e+00 1.60e-01 4.83e+01 ... (remaining 1194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 222 0.248 - 0.495: 8 0.495 - 0.743: 3 0.743 - 0.990: 3 0.990 - 1.238: 1 Chirality restraints: 237 Sorted by residual: chirality pdb=" CB VAL G 313 " pdb=" CA VAL G 313 " pdb=" CG1 VAL G 313 " pdb=" CG2 VAL G 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.39 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB VAL G 287 " pdb=" CA VAL G 287 " pdb=" CG1 VAL G 287 " pdb=" CG2 VAL G 287 " both_signs ideal model delta sigma weight residual False -2.63 -1.65 -0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CB VAL C 287 " pdb=" CA VAL C 287 " pdb=" CG1 VAL C 287 " pdb=" CG2 VAL C 287 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 234 not shown) Planarity restraints: 447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 286 " -0.024 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG ASN B 286 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 286 " -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN B 286 " 0.171 2.00e-02 2.50e+03 pdb="HD21 ASN B 286 " -0.080 2.00e-02 2.50e+03 pdb="HD22 ASN B 286 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.116 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.108 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 286 " -0.043 2.00e-02 2.50e+03 6.96e-02 7.27e+01 pdb=" CG ASN A 286 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 286 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 286 " 0.134 2.00e-02 2.50e+03 pdb="HD21 ASN A 286 " -0.020 2.00e-02 2.50e+03 pdb="HD22 ASN A 286 " -0.093 2.00e-02 2.50e+03 ... (remaining 444 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 396 2.26 - 2.84: 6035 2.84 - 3.43: 8037 3.43 - 4.01: 10197 4.01 - 4.60: 14619 Nonbonded interactions: 39284 Sorted by model distance: nonbonded pdb=" H VAL C 313 " pdb=" HA VAL C 313 " model vdw 1.669 1.816 nonbonded pdb=" HZ3 LYS G 294 " pdb=" OD2 ASP B 295 " model vdw 1.697 1.850 nonbonded pdb=" H VAL E 313 " pdb=" HA VAL E 313 " model vdw 1.701 1.816 nonbonded pdb="HG21 ILE B 277 " pdb=" H ILE B 278 " model vdw 1.719 2.270 nonbonded pdb=" H VAL G 313 " pdb=" HA VAL G 313 " model vdw 1.720 1.816 ... (remaining 39279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' } 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 945 2.51 5 N 273 2.21 5 O 288 1.98 5 H 1593 0.53 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: 0.290 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: 0.040 Extract box with map and model: 1.720 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 15.390 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.011 0.039 1527 Z= 0.743 Angle : 2.478 18.649 2043 Z= 1.587 Chirality : 0.194 1.238 237 Planarity : 0.012 0.062 258 Dihedral : 15.219 74.648 585 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 2.78 % 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: -3.56 (0.42), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.32), residues: 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.286 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.3850 time to fit residues: 13.2273 Evaluate side-chains 18 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 1527 Z= 0.297 Angle : 1.087 11.797 2043 Z= 0.571 Chirality : 0.220 1.528 237 Planarity : 0.003 0.018 258 Dihedral : 9.263 24.829 204 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer Outliers : 1.67 % 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: -3.36 (0.44), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.33), residues: 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.305 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.2519 time to fit residues: 6.0513 Evaluate side-chains 16 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0480 time to fit residues: 0.4198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 1527 Z= 0.216 Angle : 0.979 11.084 2043 Z= 0.516 Chirality : 0.217 1.462 237 Planarity : 0.003 0.020 258 Dihedral : 7.960 20.557 204 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 0.56 % 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: -2.90 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.36), residues: 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.292 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.2720 time to fit residues: 5.5208 Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0445 time to fit residues: 0.4203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.7345 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 1527 Z= 0.219 Angle : 0.952 11.293 2043 Z= 0.500 Chirality : 0.218 1.467 237 Planarity : 0.003 0.027 258 Dihedral : 7.337 19.326 204 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % 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: -2.86 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.36), residues: 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.2529 time to fit residues: 4.0274 Evaluate side-chains 12 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.7321 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 1527 Z= 0.203 Angle : 0.923 11.144 2043 Z= 0.484 Chirality : 0.217 1.468 237 Planarity : 0.003 0.028 258 Dihedral : 6.680 18.506 204 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.56 % 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: -2.64 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.295 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.2396 time to fit residues: 4.4637 Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.191 Angle : 0.905 11.064 2043 Z= 0.474 Chirality : 0.217 1.459 237 Planarity : 0.003 0.032 258 Dihedral : 6.182 17.735 204 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: -2.45 (0.53), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1920 time to fit residues: 3.3093 Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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: 0.7315 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.203 Angle : 0.907 11.272 2043 Z= 0.473 Chirality : 0.217 1.480 237 Planarity : 0.003 0.033 258 Dihedral : 6.098 17.214 204 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: -2.56 (0.53), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1692 time to fit residues: 2.9433 Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7285 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.191 Angle : 0.891 11.082 2043 Z= 0.466 Chirality : 0.217 1.471 237 Planarity : 0.003 0.032 258 Dihedral : 5.788 16.271 204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: -2.55 (0.54), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1763 time to fit residues: 3.1173 Evaluate side-chains 12 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7263 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 1527 Z= 0.192 Angle : 0.887 11.196 2043 Z= 0.463 Chirality : 0.217 1.475 237 Planarity : 0.003 0.032 258 Dihedral : 5.495 15.986 204 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -2.50 (0.54), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.303 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1954 time to fit residues: 3.7621 Evaluate side-chains 13 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7249 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 1527 Z= 0.191 Angle : 0.882 11.116 2043 Z= 0.460 Chirality : 0.217 1.465 237 Planarity : 0.003 0.032 258 Dihedral : 5.352 15.652 204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % 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: -2.51 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.304 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1769 time to fit residues: 3.4742 Evaluate side-chains 15 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.134699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.121845 restraints weight = 7317.297| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.47 r_work: 0.4316 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4307 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.4298 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work: 0.4289 rms_B_bonded: 2.45 restraints_weight: 0.0625 r_work: 0.4278 rms_B_bonded: 2.63 restraints_weight: 0.0312 r_work: 0.4266 rms_B_bonded: 2.86 restraints_weight: 0.0156 r_work: 0.4254 rms_B_bonded: 3.15 restraints_weight: 0.0078 r_work: 0.4240 rms_B_bonded: 3.51 restraints_weight: 0.0039 r_work: 0.4224 rms_B_bonded: 3.93 restraints_weight: 0.0020 r_work: 0.4206 rms_B_bonded: 4.44 restraints_weight: 0.0010 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 1527 Z= 0.208 Angle : 0.896 11.319 2043 Z= 0.466 Chirality : 0.218 1.488 237 Planarity : 0.003 0.032 258 Dihedral : 5.556 15.881 204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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: -2.57 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.42), residues: 192 =============================================================================== Job complete usr+sys time: 1767.25 seconds wall clock time: 32 minutes 8.80 seconds (1928.80 seconds total)