Starting phenix.real_space_refine on Sun Mar 10 14:31:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqk_21871/03_2024/6wqk_21871.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqk_21871/03_2024/6wqk_21871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqk_21871/03_2024/6wqk_21871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqk_21871/03_2024/6wqk_21871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqk_21871/03_2024/6wqk_21871.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqk_21871/03_2024/6wqk_21871.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1255 2.51 5 N 370 2.21 5 O 435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 276": "OD1" <-> "OD2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2070 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Time building chain proxies: 1.42, per 1000 atoms: 0.69 Number of scatterers: 2070 At special positions: 0 Unit cell: (47.88, 79.8, 42.56, 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 10 16.00 O 435 8.00 N 370 7.00 C 1255 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: 0.85 Conformation dependent library (CDL) restraints added in 390.1 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 277 removed outlier: 5.980A pdb=" N GLY B 274 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN C 277 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 276 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 274 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 277 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP A 276 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY D 274 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN E 277 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 276 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.245A pdb=" N ASN A 289 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 304 through 306 removed outlier: 6.364A pdb=" N MET A 304 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 312 through 314 removed outlier: 6.700A pdb=" N ARG A 313 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG D 313 " --> pdb=" O ASN E 314 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.43 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 730 1.34 - 1.46: 602 1.46 - 1.57: 783 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2135 Sorted by residual: bond pdb=" CA GLN E 297 " pdb=" C GLN E 297 " ideal model delta sigma weight residual 1.524 1.533 -0.010 1.26e-02 6.30e+03 5.84e-01 bond pdb=" CA GLN A 297 " pdb=" C GLN A 297 " ideal model delta sigma weight residual 1.524 1.533 -0.010 1.26e-02 6.30e+03 5.80e-01 bond pdb=" CA GLN C 297 " pdb=" C GLN C 297 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 5.27e-01 bond pdb=" CA GLN B 297 " pdb=" C GLN B 297 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 5.19e-01 bond pdb=" CA GLN D 297 " pdb=" C GLN D 297 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 5.16e-01 ... (remaining 2130 not shown) Histogram of bond angle deviations from ideal: 100.64 - 106.22: 64 106.22 - 111.81: 544 111.81 - 117.39: 636 117.39 - 122.98: 1413 122.98 - 128.56: 203 Bond angle restraints: 2860 Sorted by residual: angle pdb=" N GLY B 292 " pdb=" CA GLY B 292 " pdb=" C GLY B 292 " ideal model delta sigma weight residual 112.02 117.24 -5.22 1.86e+00 2.89e-01 7.87e+00 angle pdb=" N GLY A 292 " pdb=" CA GLY A 292 " pdb=" C GLY A 292 " ideal model delta sigma weight residual 112.02 117.23 -5.21 1.86e+00 2.89e-01 7.85e+00 angle pdb=" N GLY C 292 " pdb=" CA GLY C 292 " pdb=" C GLY C 292 " ideal model delta sigma weight residual 112.02 117.23 -5.21 1.86e+00 2.89e-01 7.84e+00 angle pdb=" N GLY E 292 " pdb=" CA GLY E 292 " pdb=" C GLY E 292 " ideal model delta sigma weight residual 112.02 117.23 -5.21 1.86e+00 2.89e-01 7.84e+00 angle pdb=" N GLY D 292 " pdb=" CA GLY D 292 " pdb=" C GLY D 292 " ideal model delta sigma weight residual 112.02 117.21 -5.19 1.86e+00 2.89e-01 7.78e+00 ... (remaining 2855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 950 13.51 - 27.03: 110 27.03 - 40.54: 30 40.54 - 54.05: 10 54.05 - 67.57: 10 Dihedral angle restraints: 1110 sinusoidal: 415 harmonic: 695 Sorted by residual: dihedral pdb=" CA ASN E 289 " pdb=" CB ASN E 289 " pdb=" CG ASN E 289 " pdb=" OD1 ASN E 289 " ideal model delta sinusoidal sigma weight residual -90.00 -157.57 67.57 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " pdb=" CG ASN C 289 " pdb=" OD1 ASN C 289 " ideal model delta sinusoidal sigma weight residual -90.00 -157.55 67.55 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN D 289 " pdb=" CB ASN D 289 " pdb=" CG ASN D 289 " pdb=" OD1 ASN D 289 " ideal model delta sinusoidal sigma weight residual -90.00 -157.52 67.52 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 1107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 80 0.020 - 0.041: 47 0.041 - 0.061: 42 0.061 - 0.081: 6 0.081 - 0.101: 10 Chirality restraints: 185 Sorted by residual: chirality pdb=" CA GLN B 297 " pdb=" N GLN B 297 " pdb=" C GLN B 297 " pdb=" CB GLN B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA GLN C 297 " pdb=" N GLN C 297 " pdb=" C GLN C 297 " pdb=" CB GLN C 297 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.55e-01 chirality pdb=" CA GLN A 297 " pdb=" N GLN A 297 " pdb=" C GLN A 297 " pdb=" CB GLN A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.49e-01 ... (remaining 182 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 300 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASN B 300 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN B 300 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 301 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 300 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASN A 300 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN A 300 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 301 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 300 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ASN C 300 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN C 300 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR C 301 " 0.009 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 652 2.80 - 3.32: 1727 3.32 - 3.85: 3702 3.85 - 4.37: 4452 4.37 - 4.90: 7957 Nonbonded interactions: 18490 Sorted by model distance: nonbonded pdb=" O SER A 285 " pdb=" OG SER B 306 " model vdw 2.272 2.440 nonbonded pdb=" O SER D 285 " pdb=" OG SER E 306 " model vdw 2.328 2.440 nonbonded pdb=" OG SER A 306 " pdb=" O SER E 285 " model vdw 2.330 2.440 nonbonded pdb=" ND2 ASN A 295 " pdb=" O PHE B 291 " model vdw 2.364 2.520 nonbonded pdb=" O SER B 285 " pdb=" OG SER C 306 " model vdw 2.373 2.440 ... (remaining 18485 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' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.090 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: 0.580 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 2135 Z= 0.208 Angle : 0.701 5.217 2860 Z= 0.405 Chirality : 0.039 0.101 185 Planarity : 0.004 0.015 430 Dihedral : 14.473 67.565 740 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % 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: -5.40 (0.23), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.17), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE A 309 TYR 0.007 0.001 TYR E 301 ARG 0.000 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.205 Fit side-chains REVERT: B 305 LYS cc_start: 0.8442 (tttt) cc_final: 0.8145 (ttpp) REVERT: E 294 TYR cc_start: 0.8439 (m-80) cc_final: 0.7825 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1314 time to fit residues: 3.9049 Evaluate side-chains 24 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN B 289 ASN D 289 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2135 Z= 0.389 Angle : 0.590 4.082 2860 Z= 0.314 Chirality : 0.046 0.115 185 Planarity : 0.004 0.032 430 Dihedral : 5.142 15.484 330 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.62 % Allowed : 10.81 % Favored : 87.57 % 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: -4.80 (0.26), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.20), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.210 Fit side-chains REVERT: C 266 ASN cc_start: 0.7942 (m-40) cc_final: 0.7706 (m-40) REVERT: D 305 LYS cc_start: 0.8293 (tttt) cc_final: 0.8090 (ttpp) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.1471 time to fit residues: 5.1303 Evaluate side-chains 31 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN E 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2135 Z= 0.169 Angle : 0.510 5.566 2860 Z= 0.261 Chirality : 0.042 0.095 185 Planarity : 0.003 0.023 430 Dihedral : 4.328 13.304 330 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.54 % Allowed : 11.35 % Favored : 88.11 % 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: -4.72 (0.27), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE D 291 TYR 0.008 0.001 TYR C 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.219 Fit side-chains REVERT: C 266 ASN cc_start: 0.7949 (m-40) cc_final: 0.7704 (m-40) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1333 time to fit residues: 4.7422 Evaluate side-chains 29 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2135 Z= 0.164 Angle : 0.514 6.062 2860 Z= 0.261 Chirality : 0.042 0.099 185 Planarity : 0.003 0.022 430 Dihedral : 4.132 12.778 330 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.54 % Allowed : 11.35 % Favored : 88.11 % 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: -4.62 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE D 309 TYR 0.010 0.001 TYR C 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.250 Fit side-chains REVERT: C 266 ASN cc_start: 0.7996 (m-40) cc_final: 0.7776 (m-40) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.1305 time to fit residues: 5.2107 Evaluate side-chains 32 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2135 Z= 0.328 Angle : 0.583 5.758 2860 Z= 0.302 Chirality : 0.045 0.124 185 Planarity : 0.004 0.031 430 Dihedral : 4.656 14.916 330 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.62 % Allowed : 11.89 % Favored : 86.49 % 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: -4.46 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.328 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.1218 time to fit residues: 5.1067 Evaluate side-chains 35 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2135 Z= 0.341 Angle : 0.599 5.782 2860 Z= 0.312 Chirality : 0.047 0.144 185 Planarity : 0.004 0.032 430 Dihedral : 4.749 14.852 330 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.16 % Allowed : 11.35 % Favored : 86.49 % 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: -4.42 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.222 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1245 time to fit residues: 5.3183 Evaluate side-chains 38 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 295 ASN E 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2135 Z= 0.249 Angle : 0.575 5.854 2860 Z= 0.296 Chirality : 0.045 0.156 185 Planarity : 0.004 0.028 430 Dihedral : 4.478 13.918 330 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 12.43 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 309 TYR 0.009 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.226 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.1234 time to fit residues: 5.2666 Evaluate side-chains 38 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2135 Z= 0.219 Angle : 0.568 5.413 2860 Z= 0.290 Chirality : 0.044 0.139 185 Planarity : 0.003 0.026 430 Dihedral : 4.342 13.604 330 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 12.97 % Favored : 85.41 % 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: -4.44 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.199 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.1145 time to fit residues: 4.9147 Evaluate side-chains 38 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 0.0270 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2135 Z= 0.357 Angle : 0.639 5.709 2860 Z= 0.332 Chirality : 0.048 0.164 185 Planarity : 0.004 0.033 430 Dihedral : 4.765 14.274 330 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.16 % Allowed : 12.43 % Favored : 85.41 % 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: -4.45 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.216 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1188 time to fit residues: 5.3681 Evaluate side-chains 39 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2135 Z= 0.224 Angle : 0.573 5.225 2860 Z= 0.294 Chirality : 0.044 0.135 185 Planarity : 0.003 0.026 430 Dihedral : 4.378 13.557 330 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.49 % 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: -4.45 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE D 309 TYR 0.009 0.001 TYR C 301 ARG 0.002 0.001 ARG B 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.213 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1229 time to fit residues: 5.1557 Evaluate side-chains 36 residues out of total 185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092725 restraints weight = 2333.756| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.95 r_work: 0.3226 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2135 Z= 0.297 Angle : 0.614 5.627 2860 Z= 0.318 Chirality : 0.047 0.138 185 Planarity : 0.004 0.030 430 Dihedral : 4.580 14.008 330 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.62 % Allowed : 12.97 % Favored : 85.41 % 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: -4.46 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 =============================================================================== Job complete usr+sys time: 854.77 seconds wall clock time: 16 minutes 7.86 seconds (967.86 seconds total)