Starting phenix.real_space_refine (version: dev) on Fri Feb 17 00:16:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/02_2023/6n3b_9350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/02_2023/6n3b_9350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/02_2023/6n3b_9350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/02_2023/6n3b_9350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/02_2023/6n3b_9350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3b_9350/02_2023/6n3b_9350.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 2735 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "C" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "E" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "I" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 260 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "J" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 287 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Time building chain proxies: 1.81, per 1000 atoms: 0.66 Number of scatterers: 2735 At special positions: 0 Unit cell: (67.032, 82.992, 48.944, 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 55 16.00 O 520 8.00 N 480 7.00 C 1680 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: 1.10 Conformation dependent library (CDL) restraints added in 465.3 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 314 through 318 removed outlier: 6.630A pdb=" N GLY C 314 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER E 317 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 316 " --> pdb=" O SER E 317 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY E 314 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER G 317 " --> pdb=" O GLY E 314 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE E 316 " --> pdb=" O SER G 317 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 314 " --> pdb=" O ALA I 315 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER I 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 316 " --> pdb=" O SER I 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.187A pdb=" N ALA A 321 " --> pdb=" O MET G 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 334 removed outlier: 5.591A pdb=" N ALA A 329 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER G 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 331 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N TRP G 334 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 333 " --> pdb=" O TRP G 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 315 through 318 removed outlier: 6.407A pdb=" N ALA B 315 " --> pdb=" O PHE H 316 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ILE H 318 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER B 317 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 321 through 323 removed outlier: 5.796A pdb=" N ALA B 321 " --> pdb=" O MET H 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.070A pdb=" N ALA D 328 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA F 328 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 330 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA B 328 " --> pdb=" O ALA J 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 337 through 343 removed outlier: 6.119A pdb=" N MET D 337 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU F 340 " --> pdb=" O MET D 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET D 339 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER F 342 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA D 341 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET F 337 " --> pdb=" O GLY H 338 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU H 340 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET F 339 " --> pdb=" O LEU H 340 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N SER H 342 " --> pdb=" O MET F 339 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA F 341 " --> pdb=" O SER H 342 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET B 337 " --> pdb=" O GLY J 338 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU J 340 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET B 339 " --> pdb=" O LEU J 340 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N SER J 342 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA B 341 " --> pdb=" O SER J 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 346 through 347 removed outlier: 3.514A pdb=" N SER D 347 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 347 " --> pdb=" O GLN H 346 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 346 " --> pdb=" O SER H 347 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 347 " --> pdb=" O GLN J 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 44 hydrogen bonds defined for protein. 132 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: 0.66 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 813 1.33 - 1.45: 450 1.45 - 1.57: 1407 1.57 - 1.69: 0 1.69 - 1.80: 110 Bond restraints: 2780 Sorted by residual: bond pdb=" CB TRP B 334 " pdb=" CG TRP B 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.18e+00 bond pdb=" CB TRP J 334 " pdb=" CG TRP J 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.15e+00 bond pdb=" CB TRP D 334 " pdb=" CG TRP D 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.13e+00 bond pdb=" CB TRP H 334 " pdb=" CG TRP H 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.12e+00 bond pdb=" CB TRP F 334 " pdb=" CG TRP F 334 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.12e+00 ... (remaining 2775 not shown) Histogram of bond angle deviations from ideal: 97.72 - 104.99: 100 104.99 - 112.26: 1226 112.26 - 119.53: 904 119.53 - 126.80: 1445 126.80 - 134.06: 50 Bond angle restraints: 3725 Sorted by residual: angle pdb=" CA ASN B 345 " pdb=" CB ASN B 345 " pdb=" CG ASN B 345 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" CA ASN F 345 " pdb=" CB ASN F 345 " pdb=" CG ASN F 345 " ideal model delta sigma weight residual 112.60 115.79 -3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" CA ASN D 345 " pdb=" CB ASN D 345 " pdb=" CG ASN D 345 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 angle pdb=" CA ASN H 345 " pdb=" CB ASN H 345 " pdb=" CG ASN H 345 " ideal model delta sigma weight residual 112.60 115.77 -3.17 1.00e+00 1.00e+00 1.00e+01 angle pdb=" CA ASN J 345 " pdb=" CB ASN J 345 " pdb=" CG ASN J 345 " ideal model delta sigma weight residual 112.60 115.76 -3.16 1.00e+00 1.00e+00 1.00e+01 ... (remaining 3720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1520 14.12 - 28.25: 125 28.25 - 42.37: 15 42.37 - 56.49: 0 56.49 - 70.61: 5 Dihedral angle restraints: 1665 sinusoidal: 600 harmonic: 1065 Sorted by residual: dihedral pdb=" CA MET H 336 " pdb=" C MET H 336 " pdb=" N MET H 337 " pdb=" CA MET H 337 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA MET J 336 " pdb=" C MET J 336 " pdb=" N MET J 337 " pdb=" CA MET J 337 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA MET B 336 " pdb=" C MET B 336 " pdb=" N MET B 337 " pdb=" CA MET B 337 " ideal model delta harmonic sigma weight residual 180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 1662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 169 0.029 - 0.057: 108 0.057 - 0.086: 38 0.086 - 0.115: 55 0.115 - 0.143: 5 Chirality restraints: 375 Sorted by residual: 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 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE J 318 " pdb=" N ILE J 318 " pdb=" C ILE J 318 " pdb=" CB ILE J 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE H 318 " pdb=" N ILE H 318 " pdb=" C ILE H 318 " pdb=" CB ILE H 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 372 not shown) Planarity restraints: 505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 348 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO H 349 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 349 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 349 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 348 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO J 349 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO J 349 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 349 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 348 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B 349 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " 0.028 5.00e-02 4.00e+02 ... (remaining 502 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 626 2.78 - 3.31: 2424 3.31 - 3.84: 4457 3.84 - 4.37: 5236 4.37 - 4.90: 9699 Nonbonded interactions: 22442 Sorted by model distance: nonbonded pdb=" O MET C 311 " pdb=" N MET E 311 " model vdw 2.253 2.520 nonbonded pdb=" N MET A 311 " pdb=" O MET G 311 " model vdw 2.253 2.520 nonbonded pdb=" O MET E 311 " pdb=" N MET G 311 " model vdw 2.254 2.520 nonbonded pdb=" O MET A 311 " pdb=" N MET I 311 " model vdw 2.254 2.520 nonbonded pdb=" O GLN B 344 " pdb=" NE2 GLN G 331 " model vdw 2.360 2.520 ... (remaining 22437 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' and resid 312 through 346) selection = (chain 'B' and resid 312 through 346) selection = (chain 'C' and resid 312 through 346) selection = (chain 'D' and resid 312 through 346) selection = (chain 'E' and resid 312 through 346) selection = (chain 'F' and resid 312 through 346) selection = (chain 'G' and resid 312 through 346) selection = (chain 'H' and resid 312 through 346) selection = (chain 'I' and resid 312 through 346) selection = (chain 'J' and resid 312 through 346) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 1680 2.51 5 N 480 2.21 5 O 520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.150 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: 0.730 Check model and map are aligned: 0.040 Process input model: 12.080 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 0.063 2780 Z= 0.672 Angle : 1.207 8.052 3725 Z= 0.650 Chirality : 0.054 0.143 375 Planarity : 0.009 0.051 505 Dihedral : 11.404 70.614 975 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.24), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.18), residues: 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1057 time to fit residues: 15.6461 Evaluate side-chains 77 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 319 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN D 319 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN I 343 GLN I 344 GLN I 346 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 2780 Z= 0.298 Angle : 0.853 15.603 3725 Z= 0.430 Chirality : 0.044 0.144 375 Planarity : 0.006 0.052 505 Dihedral : 7.066 22.919 375 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 28.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 5.28 % 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: -5.25 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.326 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.1075 time to fit residues: 13.3890 Evaluate side-chains 86 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0432 time to fit residues: 0.9932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 40.0000 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN I 346 GLN ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2780 Z= 0.297 Angle : 0.806 8.796 3725 Z= 0.416 Chirality : 0.045 0.168 375 Planarity : 0.006 0.050 505 Dihedral : 6.632 21.588 375 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer Outliers : 2.64 % 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: -5.21 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.17), residues: 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.300 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 89 average time/residue: 0.1075 time to fit residues: 12.0658 Evaluate side-chains 80 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0463 time to fit residues: 0.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 2780 Z= 0.339 Angle : 0.856 9.803 3725 Z= 0.431 Chirality : 0.045 0.143 375 Planarity : 0.006 0.051 505 Dihedral : 6.587 21.463 375 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 3.40 % 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 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.16), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.324 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.1068 time to fit residues: 11.5918 Evaluate side-chains 84 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0412 time to fit residues: 0.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2780 Z= 0.255 Angle : 0.765 8.296 3725 Z= 0.383 Chirality : 0.041 0.140 375 Planarity : 0.006 0.052 505 Dihedral : 6.204 19.602 375 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer Outliers : 2.64 % 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: -5.17 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.16), residues: 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.306 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 86 average time/residue: 0.1068 time to fit residues: 11.6479 Evaluate side-chains 81 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0438 time to fit residues: 0.6071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 32 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 331 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 2780 Z= 0.314 Angle : 0.811 8.660 3725 Z= 0.409 Chirality : 0.042 0.147 375 Planarity : 0.006 0.059 505 Dihedral : 6.248 17.491 375 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer Outliers : 1.13 % 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: -5.19 (0.21), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.16), residues: 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.286 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.1028 time to fit residues: 10.9610 Evaluate side-chains 77 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0389 time to fit residues: 0.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN C 319 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN G 319 ASN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 ASN I 346 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 2780 Z= 0.382 Angle : 0.863 8.919 3725 Z= 0.442 Chirality : 0.043 0.152 375 Planarity : 0.006 0.061 505 Dihedral : 6.550 17.791 375 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 28.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer Outliers : 1.89 % 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: -5.28 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.16), residues: 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.0994 time to fit residues: 9.9078 Evaluate side-chains 77 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0412 time to fit residues: 0.5425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN I 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2780 Z= 0.291 Angle : 0.810 8.920 3725 Z= 0.402 Chirality : 0.042 0.142 375 Planarity : 0.006 0.063 505 Dihedral : 6.208 16.240 375 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 1.89 % 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: -5.25 (0.22), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.17), residues: 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.300 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 0.1143 time to fit residues: 11.7115 Evaluate side-chains 76 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0488 time to fit residues: 0.5703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 40.0000 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2780 Z= 0.177 Angle : 0.720 9.942 3725 Z= 0.357 Chirality : 0.040 0.136 375 Planarity : 0.006 0.058 505 Dihedral : 5.695 14.369 375 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 1.89 % 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: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.17), residues: 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.305 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 94 average time/residue: 0.1121 time to fit residues: 13.3372 Evaluate side-chains 81 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0526 time to fit residues: 0.4419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 0.0000 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN H 319 ASN H 331 GLN I 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 2780 Z= 0.310 Angle : 0.857 12.262 3725 Z= 0.417 Chirality : 0.043 0.152 375 Planarity : 0.006 0.067 505 Dihedral : 5.992 15.043 375 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer Outliers : 0.75 % 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: -5.20 (0.23), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.17), residues: 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.308 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1102 time to fit residues: 11.6357 Evaluate side-chains 82 residues out of total 265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 50.0000 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN I 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.212441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.181556 restraints weight = 6898.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.183889 restraints weight = 4239.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.185355 restraints weight = 3093.717| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2780 Z= 0.247 Angle : 0.783 8.486 3725 Z= 0.388 Chirality : 0.041 0.148 375 Planarity : 0.006 0.064 505 Dihedral : 5.735 14.969 375 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer Outliers : 1.51 % 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: -5.16 (0.23), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 365 =============================================================================== Job complete usr+sys time: 823.64 seconds wall clock time: 15 minutes 50.00 seconds (950.00 seconds total)