Starting phenix.real_space_refine on Tue Feb 13 14:24:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/02_2024/7tew_25853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/02_2024/7tew_25853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/02_2024/7tew_25853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/02_2024/7tew_25853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/02_2024/7tew_25853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tew_25853/02_2024/7tew_25853.pdb" } resolution = 3.52 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= 0.013 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 37 5.16 5 C 4188 2.51 5 N 1082 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6555 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.11, per 1000 atoms: 0.63 Number of scatterers: 6555 At special positions: 0 Unit cell: (80, 86, 122, 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 37 16.00 O 1248 8.00 N 1082 7.00 C 4188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.752A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.114A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.753A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.041A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 4.045A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.697A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.928A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.811A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.521A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.689A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.289A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.511A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.328A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.648A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.614A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.896A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.002A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.774A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.158A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.347A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 915 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: 1.75 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2087 1.35 - 1.47: 1795 1.47 - 1.60: 2797 1.60 - 1.73: 0 1.73 - 1.85: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.12: 162 105.12 - 112.35: 3171 112.35 - 119.58: 2396 119.58 - 126.80: 3296 126.80 - 134.03: 128 Bond angle restraints: 9153 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.24 -5.88 1.42e+00 4.96e-01 1.71e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 122.95 -8.55 2.30e+00 1.89e-01 1.38e+01 angle pdb=" C HIS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta sigma weight residual 122.38 115.72 6.66 1.81e+00 3.05e-01 1.35e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.25 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA LYS E 31 " pdb=" CB LYS E 31 " pdb=" CG LYS E 31 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 9148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3680 16.87 - 33.74: 316 33.74 - 50.61: 51 50.61 - 67.47: 12 67.47 - 84.34: 12 Dihedral angle restraints: 4071 sinusoidal: 1733 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -47.25 -38.75 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 14.06 64.94 1 2.00e+01 2.50e-03 1.38e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.88 8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 4068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 729 0.056 - 0.111: 186 0.111 - 0.166: 51 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 976 Sorted by residual: chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 103 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 973 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO E 590 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO E 500 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.021 2.00e-02 2.50e+03 1.86e-02 6.95e+00 pdb=" CG TYR B 495 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.003 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 2224 2.86 - 3.37: 5996 3.37 - 3.88: 11266 3.88 - 4.39: 12492 4.39 - 4.90: 21655 Nonbonded interactions: 53633 Sorted by model distance: nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.344 2.520 nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.346 2.440 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.365 2.440 nonbonded pdb=" O SER E 47 " pdb=" ND2 ASN E 51 " model vdw 2.374 2.520 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.387 2.520 ... (remaining 53628 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 13.100 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.140 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.005 0.064 6737 Z= 0.314 Angle : 0.852 9.543 9153 Z= 0.488 Chirality : 0.057 0.277 976 Planarity : 0.008 0.078 1178 Dihedral : 13.336 84.341 2553 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.00 (0.25), residues: 793 helix: 0.53 (0.22), residues: 392 sheet: 0.98 (0.72), residues: 43 loop : -0.64 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 69 HIS 0.011 0.002 HIS E 34 PHE 0.027 0.003 PHE E 369 TYR 0.045 0.003 TYR B 495 ARG 0.009 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8482 (ttpt) REVERT: B 424 LYS cc_start: 0.8692 (tptt) cc_final: 0.8170 (tppt) REVERT: B 448 ASN cc_start: 0.9203 (t0) cc_final: 0.8698 (t0) REVERT: B 458 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9072 (mtmm) REVERT: B 467 ASP cc_start: 0.8432 (t0) cc_final: 0.8085 (t0) REVERT: B 473 TYR cc_start: 0.9316 (t80) cc_final: 0.9062 (t80) REVERT: B 474 GLN cc_start: 0.8885 (tt0) cc_final: 0.8616 (tt0) REVERT: E 108 LEU cc_start: 0.8613 (tp) cc_final: 0.8360 (tp) REVERT: E 249 MET cc_start: 0.8484 (ttm) cc_final: 0.8082 (mtp) REVERT: E 297 MET cc_start: 0.9202 (mtm) cc_final: 0.8996 (mtm) REVERT: E 302 TRP cc_start: 0.8366 (m-10) cc_final: 0.7320 (m100) REVERT: E 498 CYS cc_start: 0.8204 (t) cc_final: 0.7637 (t) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.2484 time to fit residues: 41.8454 Evaluate side-chains 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6737 Z= 0.274 Angle : 0.584 5.944 9153 Z= 0.308 Chirality : 0.041 0.149 976 Planarity : 0.005 0.049 1178 Dihedral : 5.664 57.845 1013 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.14 % Allowed : 9.14 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.09 (0.29), residues: 793 helix: 1.42 (0.25), residues: 415 sheet: 0.53 (0.67), residues: 52 loop : -0.05 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.017 0.002 PHE E 369 TYR 0.017 0.001 TYR B 453 ARG 0.005 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.9279 (mt) cc_final: 0.9030 (mt) REVERT: B 420 ASP cc_start: 0.8797 (m-30) cc_final: 0.8596 (m-30) REVERT: B 448 ASN cc_start: 0.9316 (t0) cc_final: 0.8908 (t0) REVERT: B 467 ASP cc_start: 0.8295 (t0) cc_final: 0.7946 (t0) REVERT: E 108 LEU cc_start: 0.8514 (tp) cc_final: 0.8122 (tp) REVERT: E 232 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8847 (mp0) REVERT: E 249 MET cc_start: 0.8460 (ttm) cc_final: 0.8100 (mtp) REVERT: E 302 TRP cc_start: 0.8535 (m-10) cc_final: 0.7690 (m100) REVERT: E 366 MET cc_start: 0.8957 (mtp) cc_final: 0.8595 (mtm) REVERT: E 435 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8781 (mp0) REVERT: E 498 CYS cc_start: 0.8843 (t) cc_final: 0.8443 (t) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.1893 time to fit residues: 20.7626 Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6737 Z= 0.222 Angle : 0.532 6.649 9153 Z= 0.273 Chirality : 0.040 0.145 976 Planarity : 0.004 0.045 1178 Dihedral : 5.223 56.758 1013 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 10.86 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.42 (0.29), residues: 793 helix: 1.71 (0.26), residues: 408 sheet: 0.30 (0.66), residues: 54 loop : 0.18 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.015 0.001 PHE E 369 TYR 0.019 0.001 TYR E 613 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 388 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8561 (t0) REVERT: B 424 LYS cc_start: 0.8735 (tptt) cc_final: 0.8261 (tppt) REVERT: B 448 ASN cc_start: 0.9295 (t0) cc_final: 0.8850 (t0) REVERT: B 467 ASP cc_start: 0.8220 (t0) cc_final: 0.7874 (t0) REVERT: E 62 MET cc_start: 0.9514 (ttp) cc_final: 0.9204 (mtm) REVERT: E 208 GLU cc_start: 0.8749 (tt0) cc_final: 0.8541 (tt0) REVERT: E 267 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9259 (mm) REVERT: E 270 MET cc_start: 0.8565 (tpp) cc_final: 0.7819 (tpp) REVERT: E 302 TRP cc_start: 0.8617 (m100) cc_final: 0.7918 (m100) REVERT: E 366 MET cc_start: 0.9009 (mtp) cc_final: 0.8683 (mtm) REVERT: E 435 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8719 (mp0) REVERT: E 437 ASN cc_start: 0.8954 (p0) cc_final: 0.8625 (m-40) REVERT: E 498 CYS cc_start: 0.8992 (t) cc_final: 0.8604 (t) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.1807 time to fit residues: 17.4503 Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 388 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6737 Z= 0.282 Angle : 0.542 5.865 9153 Z= 0.280 Chirality : 0.040 0.145 976 Planarity : 0.004 0.041 1178 Dihedral : 5.315 57.463 1013 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 11.86 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.58 (0.30), residues: 793 helix: 1.78 (0.26), residues: 408 sheet: 0.45 (0.68), residues: 52 loop : 0.34 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.016 0.002 PHE E 369 TYR 0.016 0.001 TYR B 453 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9331 (mt0) cc_final: 0.9084 (mt0) REVERT: B 424 LYS cc_start: 0.8771 (tptt) cc_final: 0.8399 (tppt) REVERT: B 448 ASN cc_start: 0.9311 (t0) cc_final: 0.8880 (t0) REVERT: B 467 ASP cc_start: 0.8169 (t0) cc_final: 0.7808 (t0) REVERT: E 208 GLU cc_start: 0.8786 (tt0) cc_final: 0.8539 (tt0) REVERT: E 270 MET cc_start: 0.8699 (tpp) cc_final: 0.8062 (tpp) REVERT: E 323 MET cc_start: 0.9558 (mmp) cc_final: 0.9356 (mmp) REVERT: E 366 MET cc_start: 0.8998 (mtp) cc_final: 0.8704 (mtp) REVERT: E 435 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8783 (mp0) REVERT: E 455 MET cc_start: 0.8970 (ttp) cc_final: 0.8506 (ttt) REVERT: E 498 CYS cc_start: 0.9291 (t) cc_final: 0.8940 (t) outliers start: 21 outliers final: 13 residues processed: 71 average time/residue: 0.1980 time to fit residues: 19.1957 Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 6737 Z= 0.380 Angle : 0.603 5.834 9153 Z= 0.313 Chirality : 0.043 0.166 976 Planarity : 0.004 0.040 1178 Dihedral : 5.698 57.241 1013 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.86 % Allowed : 13.00 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.41 (0.30), residues: 793 helix: 1.65 (0.26), residues: 408 sheet: 0.09 (0.66), residues: 52 loop : 0.30 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 302 HIS 0.006 0.001 HIS E 34 PHE 0.018 0.002 PHE E 369 TYR 0.018 0.002 TYR B 453 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.8849 (tptt) cc_final: 0.8406 (tppt) REVERT: B 448 ASN cc_start: 0.9377 (t0) cc_final: 0.8989 (t0) REVERT: B 467 ASP cc_start: 0.8076 (t0) cc_final: 0.7740 (t0) REVERT: E 62 MET cc_start: 0.9497 (ttp) cc_final: 0.9090 (mtm) REVERT: E 208 GLU cc_start: 0.8842 (tt0) cc_final: 0.8584 (tm-30) REVERT: E 249 MET cc_start: 0.8646 (ttm) cc_final: 0.8006 (mtp) REVERT: E 270 MET cc_start: 0.8543 (tpp) cc_final: 0.8264 (tpp) REVERT: E 366 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8633 (mtp) REVERT: E 498 CYS cc_start: 0.9254 (t) cc_final: 0.8961 (t) outliers start: 20 outliers final: 13 residues processed: 66 average time/residue: 0.1965 time to fit residues: 17.7254 Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6737 Z= 0.178 Angle : 0.501 6.554 9153 Z= 0.258 Chirality : 0.039 0.152 976 Planarity : 0.003 0.038 1178 Dihedral : 5.066 57.201 1013 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.43 % Allowed : 14.57 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.56 (0.30), residues: 793 helix: 1.75 (0.26), residues: 408 sheet: 0.17 (0.68), residues: 52 loop : 0.42 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.013 0.001 PHE E 369 TYR 0.010 0.001 TYR E 516 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9312 (mt0) cc_final: 0.9013 (mt0) REVERT: B 417 LYS cc_start: 0.9386 (mmmt) cc_final: 0.9080 (mmmt) REVERT: B 424 LYS cc_start: 0.8776 (tptt) cc_final: 0.8346 (tppt) REVERT: B 448 ASN cc_start: 0.9365 (t0) cc_final: 0.9096 (t0) REVERT: B 467 ASP cc_start: 0.7907 (t0) cc_final: 0.7621 (t0) REVERT: E 208 GLU cc_start: 0.8826 (tt0) cc_final: 0.8561 (tm-30) REVERT: E 270 MET cc_start: 0.8464 (tpp) cc_final: 0.8253 (tpp) REVERT: E 366 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8703 (mtp) REVERT: E 455 MET cc_start: 0.8926 (ttp) cc_final: 0.8493 (ttt) REVERT: E 498 CYS cc_start: 0.9359 (t) cc_final: 0.8911 (t) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.3020 time to fit residues: 24.6294 Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6737 Z= 0.278 Angle : 0.546 6.843 9153 Z= 0.280 Chirality : 0.041 0.154 976 Planarity : 0.004 0.039 1178 Dihedral : 5.246 57.670 1013 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.57 % Allowed : 13.86 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.56 (0.30), residues: 793 helix: 1.75 (0.26), residues: 407 sheet: 0.01 (0.68), residues: 52 loop : 0.45 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.015 0.001 PHE E 369 TYR 0.020 0.001 TYR B 473 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8338 (mp0) cc_final: 0.7863 (mp0) REVERT: B 409 GLN cc_start: 0.9299 (mt0) cc_final: 0.8959 (mt0) REVERT: B 424 LYS cc_start: 0.8821 (tptt) cc_final: 0.8381 (tppt) REVERT: B 448 ASN cc_start: 0.9402 (t0) cc_final: 0.9153 (t0) REVERT: B 467 ASP cc_start: 0.7959 (t0) cc_final: 0.7675 (t0) REVERT: E 208 GLU cc_start: 0.8873 (tt0) cc_final: 0.8626 (tm-30) REVERT: E 249 MET cc_start: 0.8520 (ttm) cc_final: 0.7994 (mtp) REVERT: E 270 MET cc_start: 0.8368 (tpp) cc_final: 0.7894 (tpp) REVERT: E 366 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8676 (mtp) REVERT: E 455 MET cc_start: 0.8950 (ttp) cc_final: 0.8456 (ttt) REVERT: E 498 CYS cc_start: 0.9314 (t) cc_final: 0.8984 (t) outliers start: 18 outliers final: 10 residues processed: 67 average time/residue: 0.1932 time to fit residues: 17.6042 Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6737 Z= 0.157 Angle : 0.495 6.401 9153 Z= 0.253 Chirality : 0.039 0.145 976 Planarity : 0.003 0.037 1178 Dihedral : 4.855 57.371 1013 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 14.71 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.65 (0.30), residues: 793 helix: 1.78 (0.26), residues: 407 sheet: 0.12 (0.69), residues: 52 loop : 0.55 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.009 0.001 TYR E 385 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8341 (mp0) cc_final: 0.7826 (mp0) REVERT: B 409 GLN cc_start: 0.9309 (mt0) cc_final: 0.9023 (mt0) REVERT: B 424 LYS cc_start: 0.8785 (tptt) cc_final: 0.8343 (tppt) REVERT: B 448 ASN cc_start: 0.9370 (t0) cc_final: 0.9123 (t0) REVERT: B 467 ASP cc_start: 0.7893 (t0) cc_final: 0.7643 (t0) REVERT: E 62 MET cc_start: 0.9409 (mtp) cc_final: 0.9088 (mtt) REVERT: E 208 GLU cc_start: 0.8855 (tt0) cc_final: 0.8593 (tm-30) REVERT: E 270 MET cc_start: 0.8408 (tpp) cc_final: 0.8010 (tpp) REVERT: E 366 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8711 (mtp) REVERT: E 455 MET cc_start: 0.8911 (ttp) cc_final: 0.8460 (ttt) REVERT: E 498 CYS cc_start: 0.9346 (t) cc_final: 0.8837 (t) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.2043 time to fit residues: 17.1913 Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6737 Z= 0.202 Angle : 0.518 7.648 9153 Z= 0.265 Chirality : 0.039 0.145 976 Planarity : 0.003 0.038 1178 Dihedral : 4.856 57.659 1013 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.86 % Allowed : 15.00 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.67 (0.30), residues: 793 helix: 1.82 (0.26), residues: 406 sheet: 0.14 (0.69), residues: 52 loop : 0.53 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.012 0.001 PHE E 369 TYR 0.021 0.001 TYR B 473 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8341 (mp0) cc_final: 0.7795 (mp0) REVERT: B 409 GLN cc_start: 0.9316 (mt0) cc_final: 0.9015 (mt0) REVERT: B 424 LYS cc_start: 0.8794 (tptt) cc_final: 0.8358 (tppt) REVERT: B 448 ASN cc_start: 0.9366 (t0) cc_final: 0.9126 (t0) REVERT: B 467 ASP cc_start: 0.7927 (t0) cc_final: 0.7692 (t0) REVERT: E 208 GLU cc_start: 0.8855 (tt0) cc_final: 0.8594 (tm-30) REVERT: E 270 MET cc_start: 0.8413 (tpp) cc_final: 0.8018 (tpp) REVERT: E 366 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8702 (mtp) REVERT: E 455 MET cc_start: 0.8914 (ttp) cc_final: 0.8452 (ttt) REVERT: E 498 CYS cc_start: 0.9329 (t) cc_final: 0.8802 (t) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.1916 time to fit residues: 15.9691 Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6737 Z= 0.166 Angle : 0.527 7.859 9153 Z= 0.267 Chirality : 0.039 0.141 976 Planarity : 0.003 0.037 1178 Dihedral : 4.688 57.640 1013 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.43 % Allowed : 15.71 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.76 (0.30), residues: 793 helix: 1.85 (0.26), residues: 407 sheet: 0.34 (0.70), residues: 51 loop : 0.59 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.009 0.001 TYR E 50 ARG 0.002 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8438 (mp0) cc_final: 0.7792 (mp0) REVERT: B 409 GLN cc_start: 0.9342 (mt0) cc_final: 0.9073 (mt0) REVERT: B 424 LYS cc_start: 0.8790 (tptt) cc_final: 0.8340 (tppt) REVERT: B 448 ASN cc_start: 0.9356 (t0) cc_final: 0.9105 (t0) REVERT: B 467 ASP cc_start: 0.7933 (t0) cc_final: 0.7723 (t0) REVERT: E 208 GLU cc_start: 0.8857 (tt0) cc_final: 0.8563 (tm-30) REVERT: E 249 MET cc_start: 0.8439 (ttm) cc_final: 0.7931 (mtp) REVERT: E 270 MET cc_start: 0.8407 (tpp) cc_final: 0.8026 (tpp) REVERT: E 366 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8716 (mtp) REVERT: E 455 MET cc_start: 0.8861 (ttp) cc_final: 0.8447 (ttt) REVERT: E 498 CYS cc_start: 0.9275 (t) cc_final: 0.8711 (t) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.1972 time to fit residues: 16.3965 Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.048479 restraints weight = 27001.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050350 restraints weight = 13881.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051615 restraints weight = 9105.830| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6737 Z= 0.201 Angle : 0.530 7.648 9153 Z= 0.269 Chirality : 0.039 0.145 976 Planarity : 0.003 0.037 1178 Dihedral : 4.742 57.774 1013 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 15.86 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.74 (0.30), residues: 793 helix: 1.85 (0.26), residues: 407 sheet: 0.26 (0.70), residues: 51 loop : 0.57 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.012 0.001 PHE E 369 TYR 0.010 0.001 TYR B 453 ARG 0.002 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1644.36 seconds wall clock time: 31 minutes 13.92 seconds (1873.92 seconds total)