Starting phenix.real_space_refine on Sun Mar 10 21:05:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkm_14047/03_2024/7qkm_14047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkm_14047/03_2024/7qkm_14047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkm_14047/03_2024/7qkm_14047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkm_14047/03_2024/7qkm_14047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkm_14047/03_2024/7qkm_14047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkm_14047/03_2024/7qkm_14047.pdb" } resolution = 2.66 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 1524 2.51 5 N 438 2.21 5 O 462 1.98 5 H 2634 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5070 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "D" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "F" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Time building chain proxies: 2.57, per 1000 atoms: 0.51 Number of scatterers: 5070 At special positions: 0 Unit cell: (93.112, 83.224, 35.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 462 8.00 N 438 7.00 C 1524 6.00 H 2634 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 517.2 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 288 removed outlier: 6.456A pdb=" N GLN B 276 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASN A 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B 278 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS A 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N LYS B 280 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP A 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N LEU B 282 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N SER A 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N LEU B 284 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N VAL A 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN B 286 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 282 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 283 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU C 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 285 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN C 286 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 287 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN C 288 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 294 removed outlier: 6.500A pdb=" N SER B 293 " --> pdb=" O LYS C 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.635A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.905A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 removed outlier: 6.496A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.146A pdb=" N GLY B 323 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 275 through 288 removed outlier: 6.949A pdb=" N GLN E 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE D 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE E 278 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN D 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS E 280 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS D 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU F 282 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP D 283 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU F 284 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER D 285 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN F 286 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL D 287 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN F 288 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 293 through 294 removed outlier: 6.528A pdb=" N SER D 293 " --> pdb=" O LYS F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.535A pdb=" N VAL D 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL F 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.920A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 319 Processing sheet with id=AB3, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.016A pdb=" N GLY D 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2622 1.12 - 1.30: 408 1.30 - 1.47: 772 1.47 - 1.64: 1274 1.64 - 1.82: 12 Bond restraints: 5088 Sorted by residual: bond pdb=" N ILE A 278 " pdb=" H ILE A 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 326 " pdb=" H GLY B 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS B 280 " pdb=" H LYS B 280 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL A 306 " pdb=" H VAL A 306 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE F 278 " pdb=" H ILE F 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 5083 not shown) Histogram of bond angle deviations from ideal: 94.87 - 101.71: 12 101.71 - 108.55: 2219 108.55 - 115.39: 4640 115.39 - 122.23: 2001 122.23 - 129.08: 446 Bond angle restraints: 9318 Sorted by residual: angle pdb=" CA LYS C 311 " pdb=" C LYS C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 118.16 121.81 -3.65 7.00e-01 2.04e+00 2.72e+01 angle pdb=" CB HIS D 299 " pdb=" CG HIS D 299 " pdb=" CD2 HIS D 299 " ideal model delta sigma weight residual 131.20 124.77 6.43 1.30e+00 5.92e-01 2.45e+01 angle pdb=" CB HIS E 299 " pdb=" CG HIS E 299 " pdb=" CD2 HIS E 299 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.39e+01 angle pdb=" CA LYS F 311 " pdb=" C LYS F 311 " pdb=" N PRO F 312 " ideal model delta sigma weight residual 118.16 121.52 -3.36 7.00e-01 2.04e+00 2.30e+01 angle pdb=" CB HIS A 299 " pdb=" CG HIS A 299 " pdb=" CD2 HIS A 299 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 ... (remaining 9313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2124 17.84 - 35.68: 120 35.68 - 53.52: 31 53.52 - 71.37: 53 71.37 - 89.21: 6 Dihedral angle restraints: 2334 sinusoidal: 1374 harmonic: 960 Sorted by residual: dihedral pdb=" CA SER B 305 " pdb=" C SER B 305 " pdb=" N VAL B 306 " pdb=" CA VAL B 306 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C SER B 289 " pdb=" N SER B 289 " pdb=" CA SER B 289 " pdb=" CB SER B 289 " ideal model delta harmonic sigma weight residual -122.60 -132.43 9.83 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA SER A 305 " pdb=" C SER A 305 " pdb=" N VAL A 306 " pdb=" CA VAL A 306 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 228 0.077 - 0.154: 108 0.154 - 0.231: 44 0.231 - 0.308: 9 0.308 - 0.385: 7 Chirality restraints: 396 Sorted by residual: chirality pdb=" CA SER B 289 " pdb=" N SER B 289 " pdb=" C SER B 289 " pdb=" CB SER B 289 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA SER D 289 " pdb=" N SER D 289 " pdb=" C SER D 289 " pdb=" CB SER D 289 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA GLN B 307 " pdb=" N GLN B 307 " pdb=" C GLN B 307 " pdb=" CB GLN B 307 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 393 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " -0.036 2.00e-02 2.50e+03 4.39e-02 2.89e+01 pdb=" CG ASN C 327 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.034 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " 0.069 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 296 " -0.003 2.00e-02 2.50e+03 4.18e-02 2.62e+01 pdb=" CG ASN D 296 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 296 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN D 296 " 0.083 2.00e-02 2.50e+03 pdb="HD21 ASN D 296 " -0.048 2.00e-02 2.50e+03 pdb="HD22 ASN D 296 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 296 " 0.036 2.00e-02 2.50e+03 3.94e-02 2.33e+01 pdb=" CG ASN E 296 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN E 296 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN E 296 " 0.032 2.00e-02 2.50e+03 pdb="HD21 ASN E 296 " -0.062 2.00e-02 2.50e+03 pdb="HD22 ASN E 296 " 0.040 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 458 2.19 - 2.79: 8995 2.79 - 3.40: 13459 3.40 - 4.00: 17923 4.00 - 4.60: 25111 Nonbonded interactions: 65946 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.591 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.603 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.608 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.618 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.620 1.850 ... (remaining 65941 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' selection = chain 'F' } 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: 3.330 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: 0.070 Extract box with map and model: 11.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.030 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.010 0.034 2454 Z= 0.695 Angle : 1.886 6.687 3282 Z= 1.229 Chirality : 0.109 0.385 396 Planarity : 0.008 0.023 408 Dihedral : 12.518 89.206 954 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS E 299 TYR 0.033 0.007 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 311 LYS cc_start: 0.8346 (mttt) cc_final: 0.8134 (mttm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 2.5913 time to fit residues: 245.8749 Evaluate side-chains 50 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2454 Z= 0.186 Angle : 0.665 3.957 3282 Z= 0.335 Chirality : 0.052 0.146 396 Planarity : 0.002 0.010 408 Dihedral : 6.068 18.160 330 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.04 % Allowed : 18.03 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 299 TYR 0.006 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8342 (tttm) cc_final: 0.7773 (pmtt) REVERT: E 294 LYS cc_start: 0.8296 (tttm) cc_final: 0.7665 (pmtt) outliers start: 6 outliers final: 1 residues processed: 54 average time/residue: 2.8739 time to fit residues: 158.2285 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.187 Angle : 0.555 4.304 3282 Z= 0.280 Chirality : 0.054 0.137 396 Planarity : 0.002 0.013 408 Dihedral : 5.487 15.307 330 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.70 % Allowed : 17.69 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.004 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8358 (tttm) cc_final: 0.7742 (pmtt) REVERT: E 294 LYS cc_start: 0.8327 (tttm) cc_final: 0.7672 (pmtt) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 2.5681 time to fit residues: 112.9888 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 307 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 14 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2454 Z= 0.131 Angle : 0.502 3.877 3282 Z= 0.252 Chirality : 0.053 0.133 396 Planarity : 0.001 0.013 408 Dihedral : 5.071 14.610 330 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.38 % Allowed : 17.01 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 TYR 0.004 0.001 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8329 (tttm) cc_final: 0.7684 (pmtt) REVERT: E 294 LYS cc_start: 0.8303 (tttm) cc_final: 0.7646 (pmtt) outliers start: 7 outliers final: 2 residues processed: 46 average time/residue: 2.4859 time to fit residues: 117.0631 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2454 Z= 0.408 Angle : 0.604 4.126 3282 Z= 0.315 Chirality : 0.057 0.157 396 Planarity : 0.002 0.013 408 Dihedral : 5.295 14.722 330 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.06 % Allowed : 16.33 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.003 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 2.6223 time to fit residues: 123.3076 Evaluate side-chains 45 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 307 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2454 Z= 0.148 Angle : 0.519 4.097 3282 Z= 0.259 Chirality : 0.054 0.137 396 Planarity : 0.001 0.012 408 Dihedral : 5.045 14.590 330 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.04 % Allowed : 18.37 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.002 0.001 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8344 (tttm) cc_final: 0.7701 (pmtt) REVERT: E 294 LYS cc_start: 0.8407 (tttm) cc_final: 0.7685 (pmtt) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 2.7151 time to fit residues: 116.5191 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain C residue 307 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2454 Z= 0.175 Angle : 0.521 5.027 3282 Z= 0.259 Chirality : 0.053 0.139 396 Planarity : 0.001 0.014 408 Dihedral : 4.887 14.070 330 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.04 % Allowed : 18.03 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 TYR 0.002 0.000 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8336 (tttm) cc_final: 0.7707 (pmtt) REVERT: E 283 ASP cc_start: 0.7368 (t0) cc_final: 0.7148 (t70) REVERT: E 294 LYS cc_start: 0.8408 (tttm) cc_final: 0.7700 (pmtt) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 2.7513 time to fit residues: 120.8164 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2454 Z= 0.157 Angle : 0.516 5.442 3282 Z= 0.256 Chirality : 0.053 0.138 396 Planarity : 0.001 0.013 408 Dihedral : 4.821 13.990 330 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.70 % Allowed : 18.03 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 TYR 0.002 0.000 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8329 (tttm) cc_final: 0.7682 (pmtt) REVERT: E 283 ASP cc_start: 0.7361 (t0) cc_final: 0.7140 (t70) REVERT: E 294 LYS cc_start: 0.8387 (tttm) cc_final: 0.7677 (pmtt) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 2.7113 time to fit residues: 116.5587 Evaluate side-chains 41 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain D residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2454 Z= 0.127 Angle : 0.503 5.989 3282 Z= 0.247 Chirality : 0.053 0.133 396 Planarity : 0.001 0.016 408 Dihedral : 4.636 13.714 330 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.02 % Allowed : 18.71 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 299 TYR 0.002 0.000 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 283 ASP cc_start: 0.7372 (t0) cc_final: 0.7147 (t70) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 2.7301 time to fit residues: 111.8996 Evaluate side-chains 38 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2454 Z= 0.121 Angle : 0.468 3.901 3282 Z= 0.235 Chirality : 0.053 0.130 396 Planarity : 0.001 0.016 408 Dihedral : 4.511 13.478 330 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.34 % Allowed : 19.05 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.001 0.000 TYR F 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 283 ASP cc_start: 0.7340 (t0) cc_final: 0.7113 (t70) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 2.4936 time to fit residues: 107.2745 Evaluate side-chains 38 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.161063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.149458 restraints weight = 8052.121| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.90 r_work: 0.4253 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2454 Z= 0.125 Angle : 0.478 3.857 3282 Z= 0.237 Chirality : 0.053 0.132 396 Planarity : 0.001 0.016 408 Dihedral : 4.453 13.400 330 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.34 % Allowed : 19.05 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.001 0.000 TYR F 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.00 seconds wall clock time: 63 minutes 56.34 seconds (3836.34 seconds total)