Starting phenix.real_space_refine on Tue Sep 24 03:09:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlv_27517/09_2024/8dlv_27517.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlv_27517/09_2024/8dlv_27517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlv_27517/09_2024/8dlv_27517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlv_27517/09_2024/8dlv_27517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlv_27517/09_2024/8dlv_27517.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlv_27517/09_2024/8dlv_27517.cif" } resolution = 3.11 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= 0.028 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 4186 2.51 5 N 1081 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 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: {'PTRANS': 27, '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: 5.49, per 1000 atoms: 0.84 Number of scatterers: 6553 At special positions: 0 Unit cell: (81, 83, 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 1249 8.00 N 1081 7.00 C 4186 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=2.04 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=2.02 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 - 3.00 Amino acid : True - 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 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: 40 helices and 6 sheets defined 58.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.358A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.448A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.667A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.004A pdb=" N ASN E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.611A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) 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: 3.721A 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: 4.033A 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 143 through 155 removed outlier: 3.881A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.718A 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 218 through 252 removed outlier: 3.764A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.784A 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: 3.632A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.671A 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: 4.197A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.527A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.320A 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: 3.595A 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 512 through 533 removed outlier: 4.474A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.902A 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: 3.995A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.803A 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 262 through 263 removed outlier: 6.092A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.075A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 912 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: 1.66 Time building geometry restraints manager: 1.98 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: 2088 1.35 - 1.47: 1815 1.47 - 1.60: 2774 1.60 - 1.73: 0 1.73 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.38e-02 5.25e+03 5.31e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 8761 2.01 - 4.02: 349 4.02 - 6.03: 30 6.03 - 8.04: 11 8.04 - 10.04: 1 Bond angle restraints: 9152 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 122.36 128.16 -5.80 1.42e+00 4.96e-01 1.67e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CA CYS E 133 " pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " ideal model delta sigma weight residual 114.40 122.20 -7.80 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.95 -3.35 1.00e+00 1.00e+00 1.12e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 3687 17.07 - 34.14: 301 34.14 - 51.21: 56 51.21 - 68.27: 14 68.27 - 85.34: 10 Dihedral angle restraints: 4068 sinusoidal: 1730 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 -51.15 -34.85 1 1.00e+01 1.00e-02 1.72e+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 15.84 63.16 1 2.00e+01 2.50e-03 1.32e+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 -131.24 8.64 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 4065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 711 0.055 - 0.110: 198 0.110 - 0.165: 56 0.165 - 0.220: 10 0.220 - 0.275: 2 Chirality restraints: 977 Sorted by residual: 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 0.28 2.00e-01 2.50e+01 1.89e+00 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 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 974 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO E 590 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 41 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.61e+00 pdb=" C TYR E 41 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR E 41 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN E 42 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO E 500 " 0.122 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 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2049 2.83 - 3.35: 5939 3.35 - 3.86: 11341 3.86 - 4.38: 12913 4.38 - 4.90: 22190 Nonbonded interactions: 54432 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.311 3.040 nonbonded pdb=" O ASP E 367 " pdb=" OG1 THR E 371 " model vdw 2.367 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.369 3.120 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.374 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.406 3.040 ... (remaining 54427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.006 0.070 6735 Z= 0.370 Angle : 0.884 10.045 9152 Z= 0.502 Chirality : 0.058 0.275 977 Planarity : 0.008 0.075 1178 Dihedral : 13.400 85.343 2550 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.29 % Allowed : 4.29 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 793 helix: 0.20 (0.22), residues: 393 sheet: 1.13 (0.73), residues: 43 loop : -0.64 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 69 HIS 0.005 0.001 HIS E 378 PHE 0.028 0.003 PHE E 369 TYR 0.033 0.002 TYR B 495 ARG 0.014 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 121 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8498 (m-30) cc_final: 0.8282 (m-30) REVERT: E 367 ASP cc_start: 0.8696 (m-30) cc_final: 0.8448 (p0) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.2785 time to fit residues: 42.9605 Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 437 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6735 Z= 0.183 Angle : 0.554 6.673 9152 Z= 0.283 Chirality : 0.040 0.143 977 Planarity : 0.005 0.042 1178 Dihedral : 5.370 52.518 1015 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.86 % Allowed : 7.86 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 793 helix: 1.25 (0.25), residues: 404 sheet: 1.09 (0.72), residues: 42 loop : -0.32 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 165 HIS 0.004 0.001 HIS E 345 PHE 0.016 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.003 0.000 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 72 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8369 (mm-30) REVERT: E 367 ASP cc_start: 0.8750 (m-30) cc_final: 0.8549 (p0) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2164 time to fit residues: 20.5522 Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6735 Z= 0.243 Angle : 0.536 6.147 9152 Z= 0.276 Chirality : 0.041 0.137 977 Planarity : 0.004 0.045 1178 Dihedral : 4.814 53.826 1013 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.14 % Allowed : 8.71 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 793 helix: 1.61 (0.26), residues: 404 sheet: 0.93 (0.75), residues: 43 loop : -0.02 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.003 0.001 HIS E 239 PHE 0.017 0.001 PHE E 369 TYR 0.014 0.001 TYR B 495 ARG 0.003 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 67 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8505 (m-30) cc_final: 0.8303 (m-30) REVERT: E 182 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8408 (mm-30) REVERT: E 270 MET cc_start: 0.9160 (tpt) cc_final: 0.8371 (tpp) REVERT: E 291 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8271 (mt) REVERT: E 367 ASP cc_start: 0.8772 (m-30) cc_final: 0.8566 (p0) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.2076 time to fit residues: 18.0989 Evaluate side-chains 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6735 Z= 0.202 Angle : 0.496 5.464 9152 Z= 0.255 Chirality : 0.040 0.160 977 Planarity : 0.004 0.039 1178 Dihedral : 4.611 54.795 1013 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.86 % Allowed : 9.71 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 793 helix: 1.79 (0.26), residues: 395 sheet: 1.06 (0.78), residues: 42 loop : 0.08 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.021 0.001 TYR E 613 ARG 0.002 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: 13 poor density : 61 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 417 LYS cc_start: 0.9155 (tptt) cc_final: 0.8893 (tptt) REVERT: B 420 ASP cc_start: 0.8512 (m-30) cc_final: 0.8210 (m-30) REVERT: B 458 LYS cc_start: 0.9126 (mppt) cc_final: 0.8843 (mmtm) REVERT: E 152 MET cc_start: 0.8673 (mmt) cc_final: 0.8435 (mmt) REVERT: E 182 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8383 (mm-30) REVERT: E 270 MET cc_start: 0.9080 (tpt) cc_final: 0.8117 (tpp) REVERT: E 291 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8152 (mm) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.2006 time to fit residues: 19.2660 Evaluate side-chains 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6735 Z= 0.247 Angle : 0.521 5.963 9152 Z= 0.268 Chirality : 0.041 0.153 977 Planarity : 0.004 0.036 1178 Dihedral : 4.614 55.411 1013 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.00 % Allowed : 10.43 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 793 helix: 1.83 (0.26), residues: 397 sheet: 1.09 (0.79), residues: 42 loop : 0.14 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.017 0.001 PHE E 369 TYR 0.011 0.001 TYR B 495 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 70 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 182 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8396 (mm-30) REVERT: E 270 MET cc_start: 0.9097 (tpt) cc_final: 0.8165 (tpp) REVERT: E 291 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8221 (mm) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.2163 time to fit residues: 19.0235 Evaluate side-chains 65 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 43 optimal weight: 0.0060 chunk 55 optimal weight: 0.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6735 Z= 0.162 Angle : 0.476 5.317 9152 Z= 0.245 Chirality : 0.039 0.155 977 Planarity : 0.003 0.037 1178 Dihedral : 4.419 55.703 1013 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.57 % Allowed : 11.43 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.30), residues: 793 helix: 1.95 (0.26), residues: 395 sheet: 1.07 (0.80), residues: 42 loop : 0.26 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.001 PHE E 369 TYR 0.032 0.001 TYR E 613 ARG 0.004 0.000 ARG B 403 *********************** 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 65 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.018 Fit side-chains REVERT: B 458 LYS cc_start: 0.9075 (mppt) cc_final: 0.8770 (mmtm) REVERT: E 182 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8369 (mm-30) REVERT: E 270 MET cc_start: 0.8989 (tpt) cc_final: 0.8206 (tpp) REVERT: E 291 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8243 (mm) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.2359 time to fit residues: 19.8331 Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6735 Z= 0.208 Angle : 0.503 6.775 9152 Z= 0.259 Chirality : 0.040 0.155 977 Planarity : 0.003 0.035 1178 Dihedral : 4.447 55.757 1013 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.29 % Allowed : 12.57 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.30), residues: 793 helix: 1.99 (0.26), residues: 395 sheet: 1.07 (0.80), residues: 42 loop : 0.34 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.017 0.001 TYR E 613 ARG 0.003 0.000 ARG B 403 *********************** 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 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.797 Fit side-chains REVERT: E 182 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8386 (mm-30) REVERT: E 270 MET cc_start: 0.9083 (tpt) cc_final: 0.8398 (tpp) REVERT: E 291 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8227 (mm) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.2037 time to fit residues: 16.1597 Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6735 Z= 0.242 Angle : 0.515 6.083 9152 Z= 0.264 Chirality : 0.041 0.154 977 Planarity : 0.004 0.033 1178 Dihedral : 4.575 56.399 1013 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.57 % Allowed : 12.43 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.30), residues: 793 helix: 1.92 (0.26), residues: 397 sheet: 1.00 (0.80), residues: 42 loop : 0.32 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.037 0.001 TYR E 613 ARG 0.003 0.000 ARG B 457 *********************** 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 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.772 Fit side-chains REVERT: E 182 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8398 (mm-30) REVERT: E 270 MET cc_start: 0.9091 (tpt) cc_final: 0.8418 (tpp) REVERT: E 291 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8212 (mm) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.2096 time to fit residues: 16.9770 Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.0070 chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6735 Z= 0.196 Angle : 0.492 5.742 9152 Z= 0.254 Chirality : 0.040 0.154 977 Planarity : 0.003 0.034 1178 Dihedral : 4.490 56.090 1013 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.57 % Allowed : 12.14 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.30), residues: 793 helix: 1.96 (0.26), residues: 394 sheet: 0.93 (0.80), residues: 42 loop : 0.36 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.014 0.001 PHE E 369 TYR 0.010 0.001 TYR B 495 ARG 0.002 0.000 ARG B 346 *********************** 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 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.706 Fit side-chains REVERT: E 182 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8384 (mm-30) REVERT: E 291 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8201 (mm) REVERT: E 467 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8353 (mt-10) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.1947 time to fit residues: 16.4176 Evaluate side-chains 60 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.0030 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6735 Z= 0.169 Angle : 0.487 5.687 9152 Z= 0.250 Chirality : 0.040 0.155 977 Planarity : 0.003 0.035 1178 Dihedral : 4.423 56.387 1013 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 12.43 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.30), residues: 793 helix: 1.96 (0.26), residues: 394 sheet: 0.90 (0.80), residues: 42 loop : 0.40 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.036 0.001 TYR E 613 ARG 0.003 0.000 ARG B 403 ********************** 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 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.713 Fit side-chains REVERT: E 182 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8373 (mm-30) REVERT: E 291 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8168 (mm) REVERT: E 366 MET cc_start: 0.8812 (ttp) cc_final: 0.8496 (ttm) REVERT: E 467 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8282 (mt-10) outliers start: 10 outliers final: 9 residues processed: 59 average time/residue: 0.1870 time to fit residues: 15.0831 Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL 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: 0.0010 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054708 restraints weight = 18678.948| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.18 r_work: 0.2741 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6735 Z= 0.153 Angle : 0.480 5.540 9152 Z= 0.247 Chirality : 0.039 0.155 977 Planarity : 0.003 0.038 1178 Dihedral : 4.352 56.598 1013 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.00 % Allowed : 13.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.30), residues: 793 helix: 2.00 (0.26), residues: 394 sheet: 0.85 (0.80), residues: 42 loop : 0.42 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.009 0.001 TYR B 495 ARG 0.003 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.51 seconds wall clock time: 31 minutes 4.38 seconds (1864.38 seconds total)