Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:12:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/11_2022/7xh8_33191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/11_2022/7xh8_33191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/11_2022/7xh8_33191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/11_2022/7xh8_33191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/11_2022/7xh8_33191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/11_2022/7xh8_33191.pdb" } resolution = 2.99 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= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3161 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 167} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Time building chain proxies: 2.34, per 1000 atoms: 0.74 Number of scatterers: 3161 At special positions: 0 Unit cell: (53, 71.02, 100.7, 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 16 16.00 O 593 8.00 N 542 7.00 C 2010 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: 1.07 Conformation dependent library (CDL) restraints added in 479.6 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 14.9% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.096A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.025A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.650A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.888A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 359 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.598A pdb=" N GLU B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET B 35 " --> pdb=" O TRP B 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.598A pdb=" N GLU B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.546A pdb=" N ILE B 106 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.526A pdb=" N ASP C 71 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.884A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 267 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: 0.84 Time building geometry restraints manager: 1.16 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: 697 1.33 - 1.45: 771 1.45 - 1.58: 1752 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3240 Sorted by residual: bond pdb=" N GLN C 90 " pdb=" CA GLN C 90 " ideal model delta sigma weight residual 1.458 1.512 -0.055 1.16e-02 7.43e+03 2.21e+01 bond pdb=" N GLN C 91 " pdb=" CA GLN C 91 " ideal model delta sigma weight residual 1.454 1.503 -0.049 1.21e-02 6.83e+03 1.65e+01 bond pdb=" N CYS B 102 " pdb=" CA CYS B 102 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.16e-02 7.43e+03 1.45e+01 bond pdb=" NE ARG B 68 " pdb=" CZ ARG B 68 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.37e+01 bond pdb=" N TYR C 92 " pdb=" CA TYR C 92 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.32e-02 5.74e+03 1.29e+01 ... (remaining 3235 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.29: 109 106.29 - 113.45: 1573 113.45 - 120.61: 1553 120.61 - 127.77: 1131 127.77 - 134.92: 35 Bond angle restraints: 4401 Sorted by residual: angle pdb=" OE1 GLN B 3 " pdb=" CD GLN B 3 " pdb=" NE2 GLN B 3 " ideal model delta sigma weight residual 122.60 117.45 5.15 1.00e+00 1.00e+00 2.66e+01 angle pdb=" OD1 ASN B 58 " pdb=" CG ASN B 58 " pdb=" ND2 ASN B 58 " ideal model delta sigma weight residual 122.60 117.46 5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" CD PRO A 373 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.34e+01 angle pdb=" CA ASP A 339 " pdb=" CB ASP A 339 " pdb=" CG ASP A 339 " ideal model delta sigma weight residual 112.60 107.82 4.78 1.00e+00 1.00e+00 2.28e+01 angle pdb=" C SER C 77 " pdb=" N ARG C 78 " pdb=" CA ARG C 78 " ideal model delta sigma weight residual 121.76 128.96 -7.20 1.51e+00 4.39e-01 2.27e+01 ... (remaining 4396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 1834 23.67 - 47.34: 59 47.34 - 71.01: 10 71.01 - 94.68: 4 94.68 - 118.34: 1 Dihedral angle restraints: 1908 sinusoidal: 735 harmonic: 1173 Sorted by residual: dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 61.66 118.34 0 5.00e+00 4.00e-02 5.60e+02 dihedral pdb=" CA TYR B 96 " pdb=" C TYR B 96 " pdb=" N CYS B 97 " pdb=" CA CYS B 97 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER C 95 " pdb=" C SER C 95 " pdb=" N PRO C 96 " pdb=" CA PRO C 96 " ideal model delta harmonic sigma weight residual 0.00 -27.70 27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 1905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 214 0.057 - 0.114: 159 0.114 - 0.170: 77 0.170 - 0.227: 22 0.227 - 0.284: 5 Chirality restraints: 477 Sorted by residual: chirality pdb=" CA ALA C 52 " pdb=" N ALA C 52 " pdb=" C ALA C 52 " pdb=" CB ALA C 52 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA SER A 514 " pdb=" N SER A 514 " pdb=" C SER A 514 " pdb=" CB SER A 514 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ASP B 109 " pdb=" N ASP B 109 " pdb=" C ASP B 109 " pdb=" CB ASP B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 474 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.145 2.00e-02 2.50e+03 8.47e-02 1.43e+02 pdb=" CG TYR A 453 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.136 2.00e-02 2.50e+03 8.39e-02 1.41e+02 pdb=" CG TYR A 489 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " -0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 97 " 0.134 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" CG TRP C 97 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 97 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 97 " -0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP C 97 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP C 97 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP C 97 " -0.103 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 97 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 97 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP C 97 " 0.105 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1360 2.96 - 3.44: 2801 3.44 - 3.93: 5495 3.93 - 4.41: 5951 4.41 - 4.90: 9884 Nonbonded interactions: 25491 Sorted by model distance: nonbonded pdb=" OE1 GLN C 90 " pdb=" OH TYR C 92 " model vdw 2.472 2.440 nonbonded pdb=" OG1 THR C 70 " pdb=" OD1 ASP C 71 " model vdw 2.533 2.440 nonbonded pdb=" OD2 ASP B 74 " pdb=" OG1 THR B 77 " model vdw 2.544 2.440 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.573 2.440 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.576 2.520 ... (remaining 25486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 16 5.16 5 C 2010 2.51 5 N 542 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 6.760 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 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 : 0.014 0.062 3240 Z= 0.938 Angle : 1.807 7.196 4401 Z= 1.188 Chirality : 0.092 0.284 477 Planarity : 0.028 0.167 567 Dihedral : 13.607 118.345 1158 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 1.01 % Allowed : 3.52 % Favored : 95.48 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.37), residues: 398 helix: -4.13 (0.47), residues: 34 sheet: -0.90 (0.43), residues: 125 loop : -0.94 (0.35), residues: 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 1.1326 time to fit residues: 139.4479 Evaluate side-chains 38 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 38 GLN C 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3240 Z= 0.254 Angle : 0.772 10.497 4401 Z= 0.390 Chirality : 0.046 0.145 477 Planarity : 0.006 0.054 567 Dihedral : 5.895 47.099 448 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.39), residues: 398 helix: -2.99 (0.70), residues: 33 sheet: -0.60 (0.40), residues: 144 loop : -0.42 (0.39), residues: 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.8593 time to fit residues: 58.8831 Evaluate side-chains 50 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.376 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.0779 time to fit residues: 0.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3240 Z= 0.216 Angle : 0.691 11.812 4401 Z= 0.340 Chirality : 0.044 0.142 477 Planarity : 0.006 0.055 567 Dihedral : 5.234 38.931 448 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.80 (0.41), residues: 398 helix: -3.06 (0.72), residues: 33 sheet: -0.31 (0.42), residues: 140 loop : -0.14 (0.42), residues: 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.9171 time to fit residues: 59.0545 Evaluate side-chains 45 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1722 time to fit residues: 0.7075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3240 Z= 0.285 Angle : 0.744 12.528 4401 Z= 0.370 Chirality : 0.045 0.154 477 Planarity : 0.005 0.047 567 Dihedral : 5.504 31.881 448 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 5.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.41), residues: 398 helix: -4.05 (0.58), residues: 25 sheet: -0.22 (0.44), residues: 135 loop : -0.57 (0.40), residues: 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 59 average time/residue: 0.8111 time to fit residues: 49.9708 Evaluate side-chains 49 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.0379 time to fit residues: 2.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3240 Z= 0.197 Angle : 0.716 12.006 4401 Z= 0.350 Chirality : 0.044 0.180 477 Planarity : 0.005 0.043 567 Dihedral : 4.934 26.609 448 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.97 (0.41), residues: 398 helix: -3.70 (0.68), residues: 25 sheet: -0.22 (0.44), residues: 135 loop : -0.48 (0.40), residues: 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 56 average time/residue: 0.8137 time to fit residues: 47.7967 Evaluate side-chains 42 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 2.4293 time to fit residues: 3.0788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3240 Z= 0.177 Angle : 0.704 12.294 4401 Z= 0.338 Chirality : 0.045 0.151 477 Planarity : 0.004 0.043 567 Dihedral : 4.575 21.418 448 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.70 (0.42), residues: 398 helix: -3.88 (0.67), residues: 25 sheet: -0.13 (0.44), residues: 133 loop : -0.18 (0.41), residues: 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 55 average time/residue: 0.8053 time to fit residues: 46.2897 Evaluate side-chains 47 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.0995 time to fit residues: 2.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.8941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 3240 Z= 0.403 Angle : 0.863 13.144 4401 Z= 0.429 Chirality : 0.048 0.161 477 Planarity : 0.006 0.068 567 Dihedral : 5.853 21.728 448 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer Outliers : 4.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.41), residues: 398 helix: -4.18 (0.52), residues: 31 sheet: -0.36 (0.44), residues: 133 loop : -0.56 (0.41), residues: 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 32 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.7263 time to fit residues: 34.4208 Evaluate side-chains 39 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1833 time to fit residues: 0.7164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.0030 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.8924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3240 Z= 0.203 Angle : 0.763 12.637 4401 Z= 0.368 Chirality : 0.045 0.163 477 Planarity : 0.005 0.055 567 Dihedral : 5.008 18.754 448 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.97 (0.42), residues: 398 helix: -4.26 (0.44), residues: 31 sheet: -0.29 (0.44), residues: 134 loop : -0.22 (0.42), residues: 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 48 average time/residue: 0.7529 time to fit residues: 38.1288 Evaluate side-chains 45 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.0697 time to fit residues: 2.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.9030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3240 Z= 0.199 Angle : 0.767 12.165 4401 Z= 0.366 Chirality : 0.045 0.163 477 Planarity : 0.005 0.050 567 Dihedral : 4.728 16.861 448 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.90 (0.42), residues: 398 helix: -4.23 (0.44), residues: 31 sheet: -0.19 (0.44), residues: 133 loop : -0.21 (0.42), residues: 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 0.6780 time to fit residues: 35.0170 Evaluate side-chains 42 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.9426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 3240 Z= 0.280 Angle : 0.834 12.400 4401 Z= 0.409 Chirality : 0.046 0.161 477 Planarity : 0.006 0.055 567 Dihedral : 5.162 16.886 448 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.98 (0.42), residues: 398 helix: -4.75 (0.35), residues: 25 sheet: -0.33 (0.45), residues: 136 loop : -0.27 (0.42), residues: 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 38 average time/residue: 0.8014 time to fit residues: 32.2053 Evaluate side-chains 36 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 24 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1945 time to fit residues: 0.7470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.070551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.063934 restraints weight = 18125.996| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.50 r_work: 0.3854 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work: 0.3841 rms_B_bonded: 4.23 restraints_weight: 0.1250 r_work: 0.3835 rms_B_bonded: 4.28 restraints_weight: 0.0625 r_work: 0.3827 rms_B_bonded: 4.37 restraints_weight: 0.0312 r_work: 0.3820 rms_B_bonded: 4.48 restraints_weight: 0.0156 r_work: 0.3812 rms_B_bonded: 4.61 restraints_weight: 0.0078 r_work: 0.3804 rms_B_bonded: 4.77 restraints_weight: 0.0039 r_work: 0.3795 rms_B_bonded: 4.95 restraints_weight: 0.0020 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.9421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3240 Z= 0.192 Angle : 0.773 13.863 4401 Z= 0.373 Chirality : 0.045 0.164 477 Planarity : 0.005 0.048 567 Dihedral : 4.689 15.393 448 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.91 (0.42), residues: 398 helix: -4.24 (0.44), residues: 31 sheet: -0.28 (0.45), residues: 134 loop : -0.16 (0.42), residues: 233 =============================================================================== Job complete usr+sys time: 1631.32 seconds wall clock time: 29 minutes 59.23 seconds (1799.23 seconds total)