Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:18:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/12_2022/6tjo_10512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/12_2022/6tjo_10512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/12_2022/6tjo_10512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/12_2022/6tjo_10512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/12_2022/6tjo_10512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/12_2022/6tjo_10512.pdb" } resolution = 3.2 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 2439 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 1.85, per 1000 atoms: 0.76 Number of scatterers: 2439 At special positions: 0 Unit cell: (105.8, 81.65, 34.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 459 8.00 N 453 7.00 C 1521 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: 0.91 Conformation dependent library (CDL) restraints added in 369.3 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 286 through 287 removed outlier: 6.326A pdb=" N ASN A 286 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.291A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.487A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.454A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 350 through 351 removed outlier: 5.840A pdb=" N VAL B 350 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.717A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.46 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 672 1.33 - 1.44: 302 1.44 - 1.55: 1492 1.55 - 1.67: 0 1.67 - 1.78: 6 Bond restraints: 2472 Sorted by residual: bond pdb=" CD LYS A 311 " pdb=" CE LYS A 311 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CD LYS C 311 " pdb=" CE LYS C 311 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.87e+00 bond pdb=" CD LYS B 311 " pdb=" CE LYS B 311 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" C LYS C 280 " pdb=" N LYS C 281 " ideal model delta sigma weight residual 1.329 1.291 0.038 1.79e-02 3.12e+03 4.39e+00 bond pdb=" C LYS B 280 " pdb=" N LYS B 281 " ideal model delta sigma weight residual 1.329 1.292 0.037 1.79e-02 3.12e+03 4.33e+00 ... (remaining 2467 not shown) Histogram of bond angle deviations from ideal: 102.71 - 108.41: 239 108.41 - 114.12: 1357 114.12 - 119.82: 585 119.82 - 125.53: 1093 125.53 - 131.23: 29 Bond angle restraints: 3303 Sorted by residual: angle pdb=" N SER C 324 " pdb=" CA SER C 324 " pdb=" C SER C 324 " ideal model delta sigma weight residual 110.80 117.73 -6.93 2.13e+00 2.20e-01 1.06e+01 angle pdb=" N SER A 324 " pdb=" CA SER A 324 " pdb=" C SER A 324 " ideal model delta sigma weight residual 110.80 117.72 -6.92 2.13e+00 2.20e-01 1.06e+01 angle pdb=" N SER B 324 " pdb=" CA SER B 324 " pdb=" C SER B 324 " ideal model delta sigma weight residual 110.80 117.71 -6.91 2.13e+00 2.20e-01 1.05e+01 angle pdb=" C LYS A 280 " pdb=" N LYS A 281 " pdb=" CA LYS A 281 " ideal model delta sigma weight residual 122.58 116.18 6.40 2.07e+00 2.33e-01 9.55e+00 angle pdb=" C LYS B 280 " pdb=" N LYS B 281 " pdb=" CA LYS B 281 " ideal model delta sigma weight residual 122.58 116.22 6.36 2.07e+00 2.33e-01 9.45e+00 ... (remaining 3298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.22: 1225 8.22 - 16.44: 218 16.44 - 24.65: 60 24.65 - 32.87: 15 32.87 - 41.09: 9 Dihedral angle restraints: 1527 sinusoidal: 642 harmonic: 885 Sorted by residual: dihedral pdb=" CA GLY B 323 " pdb=" C GLY B 323 " pdb=" N SER B 324 " pdb=" CA SER B 324 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY A 323 " pdb=" C GLY A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY C 323 " pdb=" C GLY C 323 " pdb=" N SER C 324 " pdb=" CA SER C 324 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 1524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 247 0.069 - 0.138: 113 0.138 - 0.206: 6 0.206 - 0.275: 3 0.275 - 0.344: 3 Chirality restraints: 372 Sorted by residual: chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 369 not shown) Planarity restraints: 423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 300 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO C 301 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 301 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 301 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 300 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 301 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 300 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 301 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " -0.034 5.00e-02 4.00e+02 ... (remaining 420 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 900 2.90 - 3.40: 2046 3.40 - 3.90: 3884 3.90 - 4.40: 4038 4.40 - 4.90: 8082 Nonbonded interactions: 18950 Sorted by model distance: nonbonded pdb=" N ASP A 295 " pdb=" OD1 ASP A 295 " model vdw 2.394 2.520 nonbonded pdb=" N ASP C 295 " pdb=" OD1 ASP C 295 " model vdw 2.394 2.520 nonbonded pdb=" N ASP B 295 " pdb=" OD1 ASP B 295 " model vdw 2.395 2.520 nonbonded pdb=" OD1 ASP B 314 " pdb=" N LEU B 315 " model vdw 2.525 2.520 nonbonded pdb=" OD1 ASP C 314 " pdb=" N LEU C 315 " model vdw 2.525 2.520 ... (remaining 18945 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 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1521 2.51 5 N 453 2.21 5 O 459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.510 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: 0.000 Extract box with map and model: 7.120 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.430 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.013 0.097 2472 Z= 0.833 Angle : 1.182 9.123 3303 Z= 0.614 Chirality : 0.073 0.344 372 Planarity : 0.010 0.063 423 Dihedral : 9.665 41.087 963 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % 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: -4.63 (0.32), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.25), residues: 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1588 time to fit residues: 9.5514 Evaluate side-chains 37 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 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 362 HIS B 362 HIS C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 2472 Z= 0.306 Angle : 0.681 6.196 3303 Z= 0.351 Chirality : 0.053 0.132 372 Planarity : 0.005 0.036 423 Dihedral : 6.534 26.354 327 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 3.19 % 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: -4.15 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.26), residues: 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.310 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.1708 time to fit residues: 10.3863 Evaluate side-chains 47 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0700 time to fit residues: 0.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 2472 Z= 0.308 Angle : 0.746 7.462 3303 Z= 0.367 Chirality : 0.054 0.180 372 Planarity : 0.004 0.026 423 Dihedral : 6.370 26.268 327 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer Outliers : 2.48 % 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: -3.91 (0.37), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.28), residues: 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 47 average time/residue: 0.1624 time to fit residues: 9.0831 Evaluate side-chains 43 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0301 time to fit residues: 0.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2472 Z= 0.237 Angle : 0.680 7.354 3303 Z= 0.335 Chirality : 0.052 0.220 372 Planarity : 0.003 0.020 423 Dihedral : 6.018 25.784 327 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 3.19 % 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: -3.76 (0.37), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.28), residues: 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.369 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 43 average time/residue: 0.1745 time to fit residues: 9.0385 Evaluate side-chains 36 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0286 time to fit residues: 0.5993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 2472 Z= 0.486 Angle : 0.865 14.916 3303 Z= 0.420 Chirality : 0.057 0.326 372 Planarity : 0.004 0.025 423 Dihedral : 6.685 27.596 327 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer Outliers : 2.48 % 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: -3.90 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.29), residues: 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.291 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.1570 time to fit residues: 7.4844 Evaluate side-chains 43 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2402 time to fit residues: 1.6920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2472 Z= 0.183 Angle : 0.718 11.062 3303 Z= 0.339 Chirality : 0.053 0.231 372 Planarity : 0.003 0.020 423 Dihedral : 5.751 25.480 327 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.71 % 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: -3.64 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.29), residues: 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.316 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.1634 time to fit residues: 7.0783 Evaluate side-chains 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0263 time to fit residues: 0.4879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7600 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 2472 Z= 0.383 Angle : 0.820 10.117 3303 Z= 0.394 Chirality : 0.057 0.319 372 Planarity : 0.003 0.022 423 Dihedral : 6.321 26.162 327 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer Outliers : 0.35 % 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: -3.83 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.29), residues: 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.272 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1609 time to fit residues: 6.7571 Evaluate side-chains 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7517 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2472 Z= 0.216 Angle : 0.731 9.461 3303 Z= 0.349 Chirality : 0.052 0.251 372 Planarity : 0.003 0.021 423 Dihedral : 5.808 24.580 327 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 0.35 % 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: -3.68 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.318 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1632 time to fit residues: 7.0642 Evaluate side-chains 34 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.0030 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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: 0.7496 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2472 Z= 0.209 Angle : 0.725 9.434 3303 Z= 0.347 Chirality : 0.052 0.246 372 Planarity : 0.003 0.023 423 Dihedral : 5.665 24.010 327 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % 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: -3.62 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.29), residues: 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1669 time to fit residues: 7.0803 Evaluate side-chains 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.7527 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2472 Z= 0.272 Angle : 0.754 9.738 3303 Z= 0.364 Chirality : 0.052 0.263 372 Planarity : 0.003 0.024 423 Dihedral : 5.925 24.806 327 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 0.71 % 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: -3.68 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.29), residues: 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.333 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1686 time to fit residues: 6.7204 Evaluate side-chains 34 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0266 time to fit residues: 0.5297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.094307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074484 restraints weight = 4047.936| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.06 r_work: 0.3539 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 2472 Z= 0.401 Angle : 0.832 13.289 3303 Z= 0.401 Chirality : 0.054 0.305 372 Planarity : 0.003 0.023 423 Dihedral : 6.417 25.425 327 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -3.87 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.29), residues: 315 =============================================================================== Job complete usr+sys time: 1034.85 seconds wall clock time: 19 minutes 37.39 seconds (1177.39 seconds total)