Starting phenix.real_space_refine on Tue Feb 13 13:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dma_27532/02_2024/8dma_27532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dma_27532/02_2024/8dma_27532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dma_27532/02_2024/8dma_27532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dma_27532/02_2024/8dma_27532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dma_27532/02_2024/8dma_27532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dma_27532/02_2024/8dma_27532.pdb" } resolution = 2.79 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= 0.017 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 4142 2.51 5 N 1089 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "A" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.05, per 1000 atoms: 0.62 Number of scatterers: 6487 At special positions: 0 Unit cell: (77, 87, 121, 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 1219 8.00 N 1089 7.00 C 4142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.5 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.781A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.564A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.301A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 21 through 52 removed outlier: 4.051A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.547A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.749A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.700A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 193 removed outlier: 5.092A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.706A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.658A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.622A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.557A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.709A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.868A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.615A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.449A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.605A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.743A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.242A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.159A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.539A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.993A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.273A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 882 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: 1.70 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.47: 1743 1.47 - 1.59: 2791 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6669 Sorted by residual: bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" CB VAL D 573 " pdb=" CG2 VAL D 573 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.95: 172 105.95 - 113.01: 3370 113.01 - 120.07: 2575 120.07 - 127.13: 2834 127.13 - 134.19: 107 Bond angle restraints: 9058 Sorted by residual: angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C VAL D 364 " pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " ideal model delta sigma weight residual 113.22 116.94 -3.72 1.12e+00 7.97e-01 1.10e+01 angle pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " pdb=" CG1 VAL D 364 " ideal model delta sigma weight residual 110.40 115.87 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.89e+00 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 121.44 -7.04 2.30e+00 1.89e-01 9.38e+00 ... (remaining 9053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3592 17.14 - 34.28: 334 34.28 - 51.42: 51 51.42 - 68.56: 9 68.56 - 85.70: 8 Dihedral angle restraints: 3994 sinusoidal: 1657 harmonic: 2337 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR D 445 " pdb=" C THR D 445 " pdb=" N ILE D 446 " pdb=" CA ILE D 446 " ideal model delta harmonic sigma weight residual 180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 619 0.046 - 0.092: 234 0.092 - 0.138: 81 0.138 - 0.184: 14 0.184 - 0.230: 3 Chirality restraints: 951 Sorted by residual: chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU D 182 " pdb=" N GLU D 182 " pdb=" C GLU D 182 " pdb=" CB GLU D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 558 " pdb=" CB LEU D 558 " pdb=" CD1 LEU D 558 " pdb=" CD2 LEU D 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 948 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 373 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 224 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLU D 224 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU D 224 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 225 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 468 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO D 469 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " 0.034 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1333 2.78 - 3.31: 5871 3.31 - 3.84: 11379 3.84 - 4.37: 13370 4.37 - 4.90: 22664 Nonbonded interactions: 54617 Sorted by model distance: nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.244 2.440 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.310 2.440 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.340 2.440 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.350 2.520 ... (remaining 54612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 13.390 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.100 Find NCS groups from input model: 0.160 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 6669 Z= 0.341 Angle : 0.833 9.082 9058 Z= 0.441 Chirality : 0.055 0.230 951 Planarity : 0.007 0.067 1172 Dihedral : 13.455 85.700 2474 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % 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: -1.53 (0.26), residues: 790 helix: -1.27 (0.22), residues: 399 sheet: 0.24 (0.64), residues: 60 loop : -0.69 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 163 HIS 0.005 0.002 HIS D 241 PHE 0.021 0.002 PHE D 369 TYR 0.029 0.002 TYR D 385 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.952 Fit side-chains REVERT: A 386 LYS cc_start: 0.9051 (mttt) cc_final: 0.8823 (mptt) REVERT: A 420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8478 (m-30) REVERT: D 564 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8453 (mm-30) REVERT: D 597 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 607 ASN cc_start: 0.8700 (t0) cc_final: 0.8418 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 1.3585 time to fit residues: 154.9429 Evaluate side-chains 68 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 188 ASN D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6669 Z= 0.299 Angle : 0.587 6.845 9058 Z= 0.302 Chirality : 0.044 0.184 951 Planarity : 0.005 0.047 1172 Dihedral : 6.484 59.886 932 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.73 % Allowed : 9.37 % Favored : 88.90 % 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: -0.09 (0.29), residues: 790 helix: 0.20 (0.25), residues: 396 sheet: 0.07 (0.64), residues: 59 loop : -0.21 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 163 HIS 0.005 0.001 HIS D 241 PHE 0.019 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.006 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.722 Fit side-chains REVERT: A 386 LYS cc_start: 0.9172 (mttt) cc_final: 0.8856 (mmtm) REVERT: D 182 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: D 597 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8049 (tm-30) outliers start: 12 outliers final: 4 residues processed: 79 average time/residue: 1.2441 time to fit residues: 103.8176 Evaluate side-chains 73 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6669 Z= 0.201 Angle : 0.532 6.540 9058 Z= 0.271 Chirality : 0.042 0.178 951 Planarity : 0.004 0.038 1172 Dihedral : 5.805 55.938 932 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 11.82 % Favored : 86.46 % 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: 0.54 (0.30), residues: 790 helix: 0.77 (0.26), residues: 396 sheet: 0.12 (0.66), residues: 59 loop : 0.08 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.006 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.831 Fit side-chains REVERT: A 386 LYS cc_start: 0.9181 (mttt) cc_final: 0.8874 (mtmm) REVERT: D 182 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: D 597 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 607 ASN cc_start: 0.8572 (t0) cc_final: 0.8290 (t0) outliers start: 12 outliers final: 4 residues processed: 83 average time/residue: 1.2184 time to fit residues: 106.6100 Evaluate side-chains 73 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6669 Z= 0.217 Angle : 0.543 7.538 9058 Z= 0.274 Chirality : 0.043 0.186 951 Planarity : 0.004 0.037 1172 Dihedral : 5.437 56.092 932 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 12.39 % Favored : 85.73 % 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: 0.82 (0.30), residues: 790 helix: 1.08 (0.26), residues: 390 sheet: 0.13 (0.67), residues: 59 loop : 0.13 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6616 (m110) REVERT: A 386 LYS cc_start: 0.9198 (mttt) cc_final: 0.8874 (mptt) REVERT: A 406 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8547 (mt-10) REVERT: A 493 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7661 (mmt180) REVERT: D 597 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8155 (tm-30) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 1.6406 time to fit residues: 141.9588 Evaluate side-chains 72 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6669 Z= 0.444 Angle : 0.640 9.020 9058 Z= 0.327 Chirality : 0.047 0.215 951 Planarity : 0.004 0.045 1172 Dihedral : 5.794 58.477 932 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.74 % Allowed : 13.40 % Favored : 83.86 % 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: 0.71 (0.30), residues: 790 helix: 0.87 (0.26), residues: 396 sheet: -0.06 (0.64), residues: 59 loop : 0.26 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 477 HIS 0.007 0.002 HIS D 241 PHE 0.017 0.002 PHE D 369 TYR 0.025 0.002 TYR D 381 ARG 0.008 0.001 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.6606 (m110) REVERT: A 378 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8141 (mtpm) REVERT: A 386 LYS cc_start: 0.9293 (mttt) cc_final: 0.8974 (mtmm) REVERT: A 493 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7700 (mmt180) REVERT: D 471 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: D 597 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8091 (tm-30) outliers start: 19 outliers final: 9 residues processed: 73 average time/residue: 1.4009 time to fit residues: 107.5235 Evaluate side-chains 67 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6669 Z= 0.226 Angle : 0.552 8.970 9058 Z= 0.279 Chirality : 0.043 0.215 951 Planarity : 0.004 0.044 1172 Dihedral : 5.228 56.598 932 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.88 % Allowed : 13.26 % Favored : 83.86 % 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: 0.96 (0.30), residues: 790 helix: 1.21 (0.26), residues: 390 sheet: -0.16 (0.64), residues: 59 loop : 0.27 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.012 0.001 TYR D 381 ARG 0.009 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6692 (m110) REVERT: A 378 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8174 (mtpm) REVERT: A 386 LYS cc_start: 0.9289 (mttt) cc_final: 0.8931 (mtmm) REVERT: A 406 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8546 (mt-10) REVERT: A 493 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7744 (mmt180) REVERT: D 471 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: D 472 GLN cc_start: 0.8119 (mp10) cc_final: 0.7595 (mp10) REVERT: D 597 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8084 (tm-30) outliers start: 20 outliers final: 9 residues processed: 77 average time/residue: 1.3697 time to fit residues: 110.7299 Evaluate side-chains 73 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.0020 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6669 Z= 0.274 Angle : 0.573 8.924 9058 Z= 0.289 Chirality : 0.044 0.221 951 Planarity : 0.004 0.053 1172 Dihedral : 5.174 56.816 932 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 14.41 % Favored : 83.00 % 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: 0.98 (0.30), residues: 790 helix: 1.22 (0.26), residues: 390 sheet: -0.22 (0.63), residues: 59 loop : 0.30 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.005 0.001 HIS D 241 PHE 0.017 0.001 PHE D 369 TYR 0.017 0.001 TYR D 381 ARG 0.011 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8188 (mtpm) REVERT: A 386 LYS cc_start: 0.9292 (mttt) cc_final: 0.8934 (mtmm) REVERT: A 406 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8542 (mt-10) REVERT: A 493 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7701 (mmt180) REVERT: D 471 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: D 472 GLN cc_start: 0.8108 (mp10) cc_final: 0.7648 (mp10) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 1.3565 time to fit residues: 105.4578 Evaluate side-chains 72 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 573 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: 0.9980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6669 Z= 0.208 Angle : 0.556 9.018 9058 Z= 0.279 Chirality : 0.042 0.216 951 Planarity : 0.004 0.056 1172 Dihedral : 4.956 55.845 932 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.59 % Allowed : 14.41 % Favored : 83.00 % 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: 1.08 (0.31), residues: 790 helix: 1.35 (0.26), residues: 390 sheet: -0.22 (0.62), residues: 59 loop : 0.31 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.011 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8188 (mtpm) REVERT: A 386 LYS cc_start: 0.9280 (mttt) cc_final: 0.8924 (mtmm) REVERT: A 406 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 493 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7773 (mmt180) REVERT: D 471 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: D 472 GLN cc_start: 0.8089 (mp10) cc_final: 0.7643 (mp10) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 1.3938 time to fit residues: 111.4119 Evaluate side-chains 73 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6669 Z= 0.213 Angle : 0.561 9.112 9058 Z= 0.283 Chirality : 0.042 0.221 951 Planarity : 0.004 0.060 1172 Dihedral : 4.911 55.742 932 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.02 % Allowed : 15.27 % Favored : 82.71 % 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: 1.14 (0.31), residues: 790 helix: 1.40 (0.26), residues: 391 sheet: -0.25 (0.62), residues: 59 loop : 0.34 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 477 HIS 0.004 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.013 0.001 TYR D 381 ARG 0.014 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8195 (mtpm) REVERT: A 386 LYS cc_start: 0.9279 (mttt) cc_final: 0.8879 (mptt) REVERT: A 406 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 493 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7692 (mmt180) REVERT: D 471 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: D 472 GLN cc_start: 0.8077 (mp10) cc_final: 0.7391 (mp10) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 1.3825 time to fit residues: 103.4902 Evaluate side-chains 73 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 0.0000 chunk 9 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6669 Z= 0.190 Angle : 0.562 9.363 9058 Z= 0.280 Chirality : 0.042 0.215 951 Planarity : 0.004 0.061 1172 Dihedral : 4.793 55.272 932 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 15.13 % Favored : 82.85 % 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: 1.22 (0.31), residues: 790 helix: 1.47 (0.26), residues: 392 sheet: -0.22 (0.62), residues: 59 loop : 0.37 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8206 (mtpm) REVERT: A 386 LYS cc_start: 0.9272 (mttt) cc_final: 0.8875 (mptt) REVERT: A 406 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8552 (mt-10) REVERT: A 493 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7793 (mmt180) REVERT: D 471 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: D 472 GLN cc_start: 0.8071 (mp10) cc_final: 0.7636 (mp10) REVERT: D 479 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8171 (mt-10) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 1.4057 time to fit residues: 107.8849 Evaluate side-chains 73 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 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: 0.2980 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.070585 restraints weight = 13168.903| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.80 r_work: 0.2840 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6669 Z= 0.186 Angle : 0.551 9.408 9058 Z= 0.276 Chirality : 0.042 0.213 951 Planarity : 0.004 0.064 1172 Dihedral : 4.755 55.301 932 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.87 % Allowed : 15.99 % Favored : 82.13 % 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 (0.31), residues: 790 helix: 1.54 (0.26), residues: 391 sheet: -0.23 (0.62), residues: 59 loop : 0.35 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.53 seconds wall clock time: 51 minutes 16.54 seconds (3076.54 seconds total)