Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:06:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/04_2023/7xh8_33191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/04_2023/7xh8_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_33191/04_2023/7xh8_33191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/04_2023/7xh8_33191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/04_2023/7xh8_33191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/04_2023/7xh8_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 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. 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 2.29, per 1000 atoms: 0.72 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: 1.29 Conformation dependent library (CDL) restraints added in 483.9 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: 0.27 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: 0.92 Time building geometry restraints manager: 1.34 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 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.750 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 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 : 0.388 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: 1.2822 time to fit residues: 157.5612 Evaluate side-chains 38 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5159 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3240 Z= 0.211 Angle : 0.762 11.084 4401 Z= 0.379 Chirality : 0.046 0.151 477 Planarity : 0.005 0.053 567 Dihedral : 5.742 44.921 448 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.97 (0.40), residues: 398 helix: -3.05 (0.79), residues: 27 sheet: -0.57 (0.40), residues: 143 loop : -0.26 (0.40), residues: 228 *********************** 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 71 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 1.0188 time to fit residues: 72.6776 Evaluate side-chains 50 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.388 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.0845 time to fit residues: 0.6343 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.6715 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 3240 Z= 0.297 Angle : 0.747 11.501 4401 Z= 0.375 Chirality : 0.045 0.142 477 Planarity : 0.005 0.048 567 Dihedral : 5.636 37.123 448 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.77 % Favored : 94.97 % Rotamer Outliers : 4.09 % 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: -0.89 (0.41), residues: 398 helix: -3.19 (0.68), residues: 37 sheet: -0.23 (0.43), residues: 134 loop : -0.24 (0.42), residues: 227 *********************** 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 60 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.8966 time to fit residues: 55.0393 Evaluate side-chains 47 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.1673 time to fit residues: 0.7123 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.0050 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 3240 Z= 0.343 Angle : 0.799 12.330 4401 Z= 0.395 Chirality : 0.045 0.135 477 Planarity : 0.006 0.062 567 Dihedral : 5.948 30.461 448 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 6.14 % 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: -1.28 (0.40), residues: 398 helix: -3.89 (0.60), residues: 31 sheet: -0.23 (0.43), residues: 132 loop : -0.73 (0.39), residues: 235 *********************** 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 67 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 64 average time/residue: 0.8735 time to fit residues: 58.0969 Evaluate side-chains 43 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.5505 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.8073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3240 Z= 0.214 Angle : 0.716 12.541 4401 Z= 0.349 Chirality : 0.045 0.153 477 Planarity : 0.005 0.048 567 Dihedral : 5.188 25.435 448 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % 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: -1.14 (0.41), residues: 398 helix: -3.56 (0.61), residues: 31 sheet: -0.27 (0.44), residues: 136 loop : -0.57 (0.41), residues: 231 *********************** 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 53 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.9097 time to fit residues: 50.2796 Evaluate side-chains 44 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 0.6275 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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: 0.6789 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3240 Z= 0.182 Angle : 0.711 11.569 4401 Z= 0.341 Chirality : 0.045 0.155 477 Planarity : 0.005 0.046 567 Dihedral : 4.745 21.494 448 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -0.75 (0.42), residues: 398 helix: -3.52 (0.64), residues: 31 sheet: -0.10 (0.45), residues: 136 loop : -0.19 (0.42), residues: 231 *********************** 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 55 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 53 average time/residue: 0.7922 time to fit residues: 43.9387 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: 0.1256 time to fit residues: 0.8042 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.8550 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= 0.200 Angle : 0.741 11.757 4401 Z= 0.352 Chirality : 0.045 0.159 477 Planarity : 0.004 0.046 567 Dihedral : 4.677 19.125 448 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -0.72 (0.42), residues: 398 helix: -3.89 (0.58), residues: 31 sheet: -0.14 (0.45), residues: 136 loop : -0.07 (0.42), residues: 231 *********************** 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: 14 poor density : 34 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 46 average time/residue: 0.8364 time to fit residues: 40.1699 Evaluate side-chains 46 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1212 time to fit residues: 0.7644 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.9112 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= 0.280 Angle : 0.786 12.414 4401 Z= 0.378 Chirality : 0.045 0.131 477 Planarity : 0.005 0.048 567 Dihedral : 5.348 18.980 448 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 4.39 % 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: -0.88 (0.42), residues: 398 helix: -4.18 (0.54), residues: 31 sheet: -0.16 (0.45), residues: 136 loop : -0.20 (0.42), residues: 231 *********************** 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 45 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 44 average time/residue: 0.7855 time to fit residues: 36.2733 Evaluate side-chains 41 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 0.5276 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.6880 moved from start: 0.9140 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= 0.203 Angle : 0.754 11.990 4401 Z= 0.360 Chirality : 0.045 0.133 477 Planarity : 0.005 0.047 567 Dihedral : 4.903 18.192 448 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % 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: -0.85 (0.42), residues: 398 helix: -4.22 (0.49), residues: 31 sheet: -0.16 (0.45), residues: 136 loop : -0.17 (0.42), residues: 231 *********************** 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 45 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 29 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 45 average time/residue: 0.7758 time to fit residues: 36.6093 Evaluate side-chains 41 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 0.5185 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.6903 moved from start: 0.9293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3240 Z= 0.218 Angle : 0.783 10.882 4401 Z= 0.376 Chirality : 0.045 0.132 477 Planarity : 0.005 0.047 567 Dihedral : 4.914 16.956 448 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 4.39 % 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: -0.74 (0.42), residues: 398 helix: -4.23 (0.46), residues: 31 sheet: 0.02 (0.46), residues: 136 loop : -0.16 (0.42), residues: 231 ********************** 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 43 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 28 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 42 average time/residue: 0.8192 time to fit residues: 36.0908 Evaluate side-chains 41 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 0.5137 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.070217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.064023 restraints weight = 19015.301| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 4.44 r_work: 0.3753 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.9300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3240 Z= 0.180 Angle : 0.764 10.711 4401 Z= 0.365 Chirality : 0.045 0.137 477 Planarity : 0.004 0.046 567 Dihedral : 4.567 15.092 448 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.43 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: -0.67 (0.42), residues: 398 helix: -4.18 (0.47), residues: 31 sheet: 0.09 (0.45), residues: 136 loop : -0.12 (0.41), residues: 231 =============================================================================== Job complete usr+sys time: 1745.52 seconds wall clock time: 31 minutes 36.93 seconds (1896.93 seconds total)