Starting phenix.real_space_refine on Tue Feb 13 04:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/02_2024/7xh8_33191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/02_2024/7xh8_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_33191/02_2024/7xh8_33191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/02_2024/7xh8_33191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/02_2024/7xh8_33191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xh8_33191/02_2024/7xh8_33191.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-dev-5238/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: 2.35, 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: 1.22 Conformation dependent library (CDL) restraints added in 586.4 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: 0.46 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: 0.91 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: 1.380 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: 6.600 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- 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 % Allowed : 3.80 % Favored : 95.32 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.031 TRP C 97 HIS 0.009 0.006 HIS A 505 PHE 0.087 0.017 PHE B 111 TYR 0.148 0.027 TYR A 489 ARG 0.018 0.003 ARG A 403 *********************** 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 : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 TYR cc_start: 0.7399 (m-80) cc_final: 0.6943 (m-80) outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 1.2395 time to fit residues: 152.3172 Evaluate side-chains 38 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 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: 0.6354 moved from start: 0.4678 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= 0.216 Angle : 0.761 10.720 4401 Z= 0.378 Chirality : 0.046 0.150 477 Planarity : 0.005 0.052 567 Dihedral : 5.806 48.308 448 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.75 % Allowed : 20.47 % Favored : 77.78 % 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: -0.96 (0.40), residues: 398 helix: -3.05 (0.80), residues: 27 sheet: -0.53 (0.40), residues: 142 loop : -0.27 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 36 HIS 0.000 0.000 HIS A 505 PHE 0.012 0.002 PHE C 99 TYR 0.016 0.001 TYR A 495 ARG 0.009 0.001 ARG B 86 *********************** 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 65 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 1.0355 time to fit residues: 68.4917 Evaluate side-chains 46 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 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: 0.6692 moved from start: 0.6455 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= 0.295 Angle : 0.746 11.202 4401 Z= 0.373 Chirality : 0.045 0.138 477 Planarity : 0.005 0.051 567 Dihedral : 5.633 38.794 448 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.09 % Allowed : 17.54 % Favored : 78.36 % 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: -0.91 (0.41), residues: 398 helix: -3.17 (0.68), residues: 37 sheet: -0.27 (0.43), residues: 134 loop : -0.24 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 36 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.002 PHE C 72 TYR 0.017 0.002 TYR A 495 ARG 0.008 0.001 ARG B 73 *********************** 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: 14 poor density : 49 time to evaluate : 0.527 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.9115 time to fit residues: 58.9294 Evaluate side-chains 44 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.6913 moved from start: 0.7882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 3240 Z= 0.373 Angle : 0.814 12.034 4401 Z= 0.404 Chirality : 0.046 0.150 477 Planarity : 0.006 0.061 567 Dihedral : 6.092 32.158 448 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.56 % Allowed : 19.88 % Favored : 74.56 % 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: -1.39 (0.40), residues: 398 helix: -3.91 (0.61), residues: 31 sheet: -0.36 (0.43), residues: 133 loop : -0.77 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 114 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.002 PHE C 37 TYR 0.027 0.002 TYR A 369 ARG 0.011 0.001 ARG B 86 *********************** 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 62 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.7589 (mt) cc_final: 0.7136 (tp) REVERT: B 38 VAL cc_start: 0.8339 (t) cc_final: 0.7764 (p) outliers start: 19 outliers final: 9 residues processed: 59 average time/residue: 1.0497 time to fit residues: 63.9551 Evaluate side-chains 43 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.6943 moved from start: 0.8437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3240 Z= 0.314 Angle : 0.764 12.780 4401 Z= 0.384 Chirality : 0.045 0.144 477 Planarity : 0.006 0.053 567 Dihedral : 5.881 26.224 448 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.09 % Allowed : 22.81 % Favored : 73.10 % 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: -1.57 (0.41), residues: 398 helix: -4.09 (0.50), residues: 31 sheet: -0.56 (0.44), residues: 135 loop : -0.84 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 114 HIS 0.000 0.000 HIS A 505 PHE 0.015 0.002 PHE B 65 TYR 0.017 0.002 TYR A 369 ARG 0.008 0.001 ARG C 55 *********************** 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 51 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 TRP cc_start: 0.7831 (m-10) cc_final: 0.7571 (m-10) outliers start: 14 outliers final: 8 residues processed: 50 average time/residue: 0.9215 time to fit residues: 47.9111 Evaluate side-chains 37 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.8523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3240 Z= 0.194 Angle : 0.727 12.472 4401 Z= 0.351 Chirality : 0.046 0.146 477 Planarity : 0.005 0.049 567 Dihedral : 5.140 22.156 448 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.92 % Allowed : 22.81 % Favored : 74.27 % 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: -1.12 (0.42), residues: 398 helix: -3.89 (0.59), residues: 31 sheet: -0.45 (0.45), residues: 136 loop : -0.36 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 37 HIS 0.000 0.000 HIS A 505 PHE 0.017 0.002 PHE B 65 TYR 0.014 0.001 TYR A 495 ARG 0.006 0.001 ARG C 55 *********************** 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 47 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 TRP cc_start: 0.7778 (m-10) cc_final: 0.7568 (m-10) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.8217 time to fit residues: 38.7275 Evaluate side-chains 40 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.6992 moved from start: 0.9131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3240 Z= 0.315 Angle : 0.813 12.916 4401 Z= 0.396 Chirality : 0.045 0.146 477 Planarity : 0.005 0.058 567 Dihedral : 5.756 21.661 448 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.22 % Allowed : 21.93 % Favored : 74.85 % 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: -1.23 (0.42), residues: 398 helix: -4.33 (0.69), residues: 19 sheet: -0.49 (0.44), residues: 136 loop : -0.65 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 114 HIS 0.001 0.000 HIS A 505 PHE 0.015 0.002 PHE B 65 TYR 0.013 0.002 TYR A 451 ARG 0.008 0.001 ARG C 55 *********************** 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 41 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.8147 time to fit residues: 32.4999 Evaluate side-chains 36 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 86 VAL 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: 3.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.6898 moved from start: 0.9129 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 : 0.766 12.399 4401 Z= 0.364 Chirality : 0.045 0.155 477 Planarity : 0.005 0.051 567 Dihedral : 5.042 19.153 448 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.22 % Allowed : 21.64 % Favored : 75.15 % 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: -1.01 (0.42), residues: 398 helix: -4.09 (0.62), residues: 25 sheet: -0.39 (0.44), residues: 136 loop : -0.35 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 114 HIS 0.000 0.000 HIS A 505 PHE 0.019 0.002 PHE B 65 TYR 0.013 0.001 TYR B 81 ARG 0.005 0.001 ARG C 55 *********************** 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 47 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.8349 time to fit residues: 39.1908 Evaluate side-chains 39 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 3 optimal weight: 0.0570 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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: 0.6838 moved from start: 0.9119 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= 0.184 Angle : 0.752 12.204 4401 Z= 0.357 Chirality : 0.045 0.159 477 Planarity : 0.005 0.049 567 Dihedral : 4.638 16.911 448 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.46 % Allowed : 23.98 % Favored : 74.56 % 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: -0.82 (0.42), residues: 398 helix: -4.08 (0.61), residues: 25 sheet: -0.28 (0.44), residues: 136 loop : -0.20 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 114 HIS 0.001 0.001 HIS A 505 PHE 0.017 0.002 PHE B 65 TYR 0.011 0.001 TYR A 495 ARG 0.004 0.001 ARG C 55 *********************** 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 39 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 36 average time/residue: 1.0025 time to fit residues: 37.5417 Evaluate side-chains 37 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 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: 0.6874 moved from start: 0.9301 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= 0.200 Angle : 0.758 11.338 4401 Z= 0.360 Chirality : 0.045 0.139 477 Planarity : 0.005 0.051 567 Dihedral : 4.691 17.710 448 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.05 % Allowed : 23.68 % Favored : 74.27 % 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: -4.15 (0.59), residues: 25 sheet: -0.20 (0.44), residues: 136 loop : -0.13 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 114 HIS 0.001 0.000 HIS A 505 PHE 0.017 0.001 PHE B 65 TYR 0.010 0.001 TYR A 495 ARG 0.004 0.001 ARG C 55 ********************** 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 38 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 1.1396 time to fit residues: 40.7429 Evaluate side-chains 34 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.069522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.063430 restraints weight = 19364.142| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 4.37 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.9391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3240 Z= 0.229 Angle : 0.772 11.273 4401 Z= 0.372 Chirality : 0.045 0.195 477 Planarity : 0.005 0.053 567 Dihedral : 4.873 21.465 448 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.63 % Allowed : 23.39 % Favored : 73.98 % 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: -0.66 (0.42), residues: 398 helix: -4.15 (0.60), residues: 25 sheet: -0.15 (0.44), residues: 136 loop : -0.07 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 114 HIS 0.001 0.000 HIS A 505 PHE 0.016 0.002 PHE B 65 TYR 0.012 0.001 TYR C 92 ARG 0.005 0.001 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.58 seconds wall clock time: 31 minutes 14.84 seconds (1874.84 seconds total)