Starting phenix.real_space_refine on Sun Mar 10 14:34:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py2_13708/03_2024/7py2_13708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py2_13708/03_2024/7py2_13708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py2_13708/03_2024/7py2_13708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py2_13708/03_2024/7py2_13708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py2_13708/03_2024/7py2_13708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py2_13708/03_2024/7py2_13708.pdb" } resolution = 2.59 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 1264 2.51 5 N 420 2.21 5 O 436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 538 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 538 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 538 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 538 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Time building chain proxies: 1.34, per 1000 atoms: 0.62 Number of scatterers: 2152 At special positions: 0 Unit cell: (79.05, 67.89, 40.92, 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 32 16.00 O 436 8.00 N 420 7.00 C 1264 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: 0.84 Conformation dependent library (CDL) restraints added in 448.4 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 472 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.524A pdb=" N GLY A 284 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY C 284 " --> pdb=" O ASN D 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 298 through 299 removed outlier: 5.853A pdb=" N GLY A 298 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLY C 298 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 302 through 303 removed outlier: 6.660A pdb=" N ASN A 302 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 313 removed outlier: 6.669A pdb=" N ASN A 312 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 312 " --> pdb=" O PHE D 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 329 removed outlier: 8.352A pdb=" N GLN A 327 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 329 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLN C 327 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 343 removed outlier: 6.920A pdb=" N GLN B 343 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER A 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N MET D 336 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 335 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY D 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N MET A 337 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU D 340 " --> pdb=" O MET A 337 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET A 339 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER D 342 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ALA A 341 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN D 343 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.744A pdb=" N GLN A 346 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 356 removed outlier: 6.897A pdb=" N GLN A 354 " --> pdb=" O ASN D 355 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 662 1.34 - 1.46: 325 1.46 - 1.59: 1129 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 2180 Sorted by residual: bond pdb=" C ALA C 321 " pdb=" O ALA C 321 " ideal model delta sigma weight residual 1.232 1.292 -0.060 1.34e-02 5.57e+03 2.00e+01 bond pdb=" C ALA D 321 " pdb=" O ALA D 321 " ideal model delta sigma weight residual 1.232 1.291 -0.060 1.34e-02 5.57e+03 2.00e+01 bond pdb=" C ALA A 321 " pdb=" O ALA A 321 " ideal model delta sigma weight residual 1.232 1.291 -0.060 1.34e-02 5.57e+03 1.98e+01 bond pdb=" C ALA B 321 " pdb=" O ALA B 321 " ideal model delta sigma weight residual 1.232 1.291 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" N GLY A 348 " pdb=" CA GLY A 348 " ideal model delta sigma weight residual 1.434 1.477 -0.044 1.22e-02 6.72e+03 1.28e+01 ... (remaining 2175 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.55: 72 106.55 - 113.35: 954 113.35 - 120.16: 958 120.16 - 126.97: 884 126.97 - 133.77: 32 Bond angle restraints: 2900 Sorted by residual: angle pdb=" C ARG D 293 " pdb=" N GLY D 294 " pdb=" CA GLY D 294 " ideal model delta sigma weight residual 119.92 124.57 -4.65 9.60e-01 1.09e+00 2.35e+01 angle pdb=" C ARG A 293 " pdb=" N GLY A 294 " pdb=" CA GLY A 294 " ideal model delta sigma weight residual 119.92 124.55 -4.63 9.60e-01 1.09e+00 2.33e+01 angle pdb=" C ARG C 293 " pdb=" N GLY C 294 " pdb=" CA GLY C 294 " ideal model delta sigma weight residual 119.92 124.55 -4.63 9.60e-01 1.09e+00 2.33e+01 angle pdb=" C ARG B 293 " pdb=" N GLY B 294 " pdb=" CA GLY B 294 " ideal model delta sigma weight residual 119.92 124.53 -4.61 9.60e-01 1.09e+00 2.30e+01 angle pdb=" C LEU B 330 " pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 122.34 128.90 -6.56 1.39e+00 5.18e-01 2.23e+01 ... (remaining 2895 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.20: 1080 17.20 - 34.38: 116 34.38 - 51.57: 36 51.57 - 68.76: 4 68.76 - 85.95: 8 Dihedral angle restraints: 1244 sinusoidal: 460 harmonic: 784 Sorted by residual: dihedral pdb=" CA GLY B 284 " pdb=" C GLY B 284 " pdb=" N ASN B 285 " pdb=" CA ASN B 285 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY D 284 " pdb=" C GLY D 284 " pdb=" N ASN D 285 " pdb=" CA ASN D 285 " ideal model delta harmonic sigma weight residual 180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY A 284 " pdb=" C GLY A 284 " pdb=" N ASN A 285 " pdb=" CA ASN A 285 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 1241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 102 0.044 - 0.088: 82 0.088 - 0.132: 48 0.132 - 0.176: 16 0.176 - 0.220: 4 Chirality restraints: 252 Sorted by residual: chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE D 318 " pdb=" N ILE D 318 " pdb=" C ILE D 318 " pdb=" CB ILE D 318 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 249 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 336 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C MET C 336 " 0.033 2.00e-02 2.50e+03 pdb=" O MET C 336 " -0.013 2.00e-02 2.50e+03 pdb=" N MET C 337 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 336 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C MET D 336 " 0.033 2.00e-02 2.50e+03 pdb=" O MET D 336 " -0.013 2.00e-02 2.50e+03 pdb=" N MET D 337 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 336 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C MET A 336 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 336 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 337 " -0.011 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 761 2.92 - 3.41: 2046 3.41 - 3.91: 3535 3.91 - 4.40: 4076 4.40 - 4.90: 7455 Nonbonded interactions: 17873 Sorted by model distance: nonbonded pdb=" O ASN C 355 " pdb=" ND2 ASN D 358 " model vdw 2.423 2.520 nonbonded pdb=" ND2 ASN A 358 " pdb=" O ASN D 355 " model vdw 2.423 2.520 nonbonded pdb=" O ASN A 355 " pdb=" ND2 ASN B 358 " model vdw 2.424 2.520 nonbonded pdb=" OG SER A 333 " pdb=" O GLY B 300 " model vdw 2.559 2.440 nonbonded pdb=" O GLY A 300 " pdb=" OG SER D 333 " model vdw 2.559 2.440 ... (remaining 17868 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' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.430 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.160 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.015 0.060 2180 Z= 1.017 Angle : 1.835 6.975 2900 Z= 1.282 Chirality : 0.079 0.220 252 Planarity : 0.007 0.019 432 Dihedral : 17.258 85.948 772 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.00 % Allowed : 8.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP B 334 PHE 0.017 0.006 PHE D 289 ARG 0.002 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.239 Fit side-chains REVERT: A 293 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8336 (mmt90) REVERT: A 339 MET cc_start: 0.8144 (ttt) cc_final: 0.7915 (ttp) REVERT: B 359 MET cc_start: 0.8258 (ttt) cc_final: 0.8030 (mtp) REVERT: C 293 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8543 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 1.3740 time to fit residues: 94.9837 Evaluate side-chains 51 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 286 GLN C 346 GLN D 286 GLN D 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2180 Z= 0.190 Angle : 0.608 4.687 2900 Z= 0.328 Chirality : 0.041 0.129 252 Planarity : 0.003 0.021 432 Dihedral : 5.291 14.897 316 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.00 % Allowed : 19.50 % Favored : 75.50 % 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: -4.60 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 334 PHE 0.010 0.001 PHE A 313 ARG 0.002 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.225 Fit side-chains REVERT: A 293 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8333 (mmt90) REVERT: B 359 MET cc_start: 0.8172 (ttt) cc_final: 0.7962 (mtp) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 1.5242 time to fit residues: 89.8251 Evaluate side-chains 56 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain C residue 342 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2180 Z= 0.329 Angle : 0.689 5.174 2900 Z= 0.377 Chirality : 0.047 0.124 252 Planarity : 0.003 0.024 432 Dihedral : 5.164 14.960 316 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.50 % Allowed : 19.00 % Favored : 75.50 % 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: -4.30 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 334 PHE 0.011 0.002 PHE B 283 ARG 0.002 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.237 Fit side-chains REVERT: B 293 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8389 (mmt90) REVERT: B 337 MET cc_start: 0.8778 (ttm) cc_final: 0.8504 (ttm) outliers start: 11 outliers final: 2 residues processed: 60 average time/residue: 1.6369 time to fit residues: 99.6426 Evaluate side-chains 60 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 317 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.4980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 354 GLN C 286 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2180 Z= 0.241 Angle : 0.628 4.526 2900 Z= 0.342 Chirality : 0.044 0.124 252 Planarity : 0.003 0.019 432 Dihedral : 4.994 15.037 316 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.00 % Allowed : 15.50 % Favored : 76.50 % 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: -4.16 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.007 0.001 PHE B 283 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.237 Fit side-chains REVERT: B 293 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8355 (mmt90) REVERT: B 337 MET cc_start: 0.8776 (ttm) cc_final: 0.8510 (ttm) outliers start: 16 outliers final: 6 residues processed: 62 average time/residue: 1.5214 time to fit residues: 95.7731 Evaluate side-chains 64 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 overall best weight: 2.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2180 Z= 0.252 Angle : 0.634 4.496 2900 Z= 0.345 Chirality : 0.044 0.122 252 Planarity : 0.003 0.017 432 Dihedral : 4.944 15.012 316 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 7.50 % Allowed : 15.50 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.007 0.001 PHE B 283 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.241 Fit side-chains REVERT: B 293 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8371 (mmt90) REVERT: B 337 MET cc_start: 0.8752 (ttm) cc_final: 0.8498 (ttm) outliers start: 15 outliers final: 6 residues processed: 60 average time/residue: 1.5374 time to fit residues: 93.6677 Evaluate side-chains 63 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2180 Z= 0.169 Angle : 0.574 3.894 2900 Z= 0.310 Chirality : 0.042 0.122 252 Planarity : 0.002 0.017 432 Dihedral : 4.743 14.769 316 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.50 % Allowed : 17.50 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.006 0.001 PHE B 289 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.250 Fit side-chains REVERT: B 293 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8376 (mmt90) REVERT: B 337 MET cc_start: 0.8736 (ttm) cc_final: 0.8490 (ttm) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 1.5497 time to fit residues: 99.1066 Evaluate side-chains 67 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2180 Z= 0.264 Angle : 0.637 4.209 2900 Z= 0.345 Chirality : 0.044 0.122 252 Planarity : 0.003 0.017 432 Dihedral : 4.781 14.707 316 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.00 % Allowed : 16.50 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 334 PHE 0.007 0.001 PHE B 289 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.182 Fit side-chains REVERT: A 330 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8388 (tt) REVERT: B 293 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8385 (mmt90) REVERT: B 337 MET cc_start: 0.8754 (ttm) cc_final: 0.8505 (ttm) outliers start: 16 outliers final: 7 residues processed: 59 average time/residue: 1.5072 time to fit residues: 90.2605 Evaluate side-chains 66 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2180 Z= 0.387 Angle : 0.728 4.952 2900 Z= 0.396 Chirality : 0.048 0.126 252 Planarity : 0.003 0.017 432 Dihedral : 5.113 14.950 316 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 7.00 % Allowed : 18.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.009 0.002 PHE B 283 ARG 0.001 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.222 Fit side-chains REVERT: A 330 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8426 (tt) REVERT: B 293 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8435 (mmt90) REVERT: B 337 MET cc_start: 0.8777 (ttm) cc_final: 0.8523 (ttm) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 1.4159 time to fit residues: 86.2831 Evaluate side-chains 67 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2180 Z= 0.230 Angle : 0.638 4.121 2900 Z= 0.344 Chirality : 0.044 0.123 252 Planarity : 0.003 0.016 432 Dihedral : 4.987 15.314 316 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 7.50 % Allowed : 18.00 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 334 PHE 0.007 0.001 PHE B 289 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.236 Fit side-chains REVERT: A 330 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8454 (tt) REVERT: A 336 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8332 (ttt) REVERT: B 293 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8417 (mmt90) REVERT: B 337 MET cc_start: 0.8748 (ttm) cc_final: 0.8492 (ttm) outliers start: 15 outliers final: 6 residues processed: 60 average time/residue: 1.5889 time to fit residues: 96.7924 Evaluate side-chains 66 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2180 Z= 0.391 Angle : 0.731 4.871 2900 Z= 0.396 Chirality : 0.048 0.128 252 Planarity : 0.003 0.017 432 Dihedral : 5.109 14.792 316 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 7.00 % Allowed : 19.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.18), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.009 0.002 PHE B 283 ARG 0.001 0.000 ARG D 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.260 Fit side-chains REVERT: A 330 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8456 (tt) REVERT: A 336 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8370 (ttt) REVERT: B 293 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8453 (mmt90) REVERT: B 337 MET cc_start: 0.8773 (ttm) cc_final: 0.8520 (ttm) outliers start: 14 outliers final: 8 residues processed: 58 average time/residue: 1.6259 time to fit residues: 95.9039 Evaluate side-chains 66 residues out of total 200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088220 restraints weight = 2479.108| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.57 r_work: 0.3267 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2180 Z= 0.421 Angle : 0.751 5.046 2900 Z= 0.407 Chirality : 0.050 0.136 252 Planarity : 0.003 0.017 432 Dihedral : 5.182 14.707 316 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 8.50 % Allowed : 17.00 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.18), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.009 0.002 PHE B 283 ARG 0.002 0.000 ARG D 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.50 seconds wall clock time: 32 minutes 56.78 seconds (1976.78 seconds total)