Starting phenix.real_space_refine on Sun Mar 10 22:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sla_25196/03_2024/7sla_25196_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sla_25196/03_2024/7sla_25196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sla_25196/03_2024/7sla_25196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sla_25196/03_2024/7sla_25196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sla_25196/03_2024/7sla_25196_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sla_25196/03_2024/7sla_25196_neut.pdb" } resolution = 3.15 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= -0.002 sd= 0.071 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 3601 2.51 5 N 877 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5458 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4512 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 22, 'TRANS': 562} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.77, per 1000 atoms: 0.69 Number of scatterers: 5458 At special positions: 0 Unit cell: (96.05, 84.15, 111.35, 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 943 8.00 N 877 7.00 C 3601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1290 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 59.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.911A pdb=" N ILE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.672A pdb=" N GLY A 99 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.890A pdb=" N VAL A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 128 through 136 removed outlier: 3.506A pdb=" N LYS A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 4.147A pdb=" N VAL A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 Processing helix chain 'A' and resid 177 through 194 removed outlier: 4.032A pdb=" N ILE A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 removed outlier: 4.103A pdb=" N LEU A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.605A pdb=" N MET A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.635A pdb=" N CYS A 255 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 275 through 293 removed outlier: 3.554A pdb=" N ILE A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.961A pdb=" N LYS A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.723A pdb=" N MET A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.728A pdb=" N GLU A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.736A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 409 removed outlier: 4.041A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 418 through 428 removed outlier: 3.594A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 Proline residue: A 442 - end of helix removed outlier: 3.632A pdb=" N GLN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.982A pdb=" N TYR A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 477 removed outlier: 4.179A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.734A pdb=" N ALA A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TRP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 546 removed outlier: 4.380A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 664 removed outlier: 3.707A pdb=" N ALA A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.568A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.066A pdb=" N GLY B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 39 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 50 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.505A pdb=" N LEU B 20 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET B 84 " --> pdb=" O LEU B 20 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 729 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: 1.42 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 827 1.31 - 1.44: 1570 1.44 - 1.57: 3136 1.57 - 1.70: 0 1.70 - 1.83: 59 Bond restraints: 5592 Sorted by residual: bond pdb=" C ILE A 397 " pdb=" O ILE A 397 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.79e+01 bond pdb=" CA SER A 393 " pdb=" C SER A 393 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" N SER A 393 " pdb=" CA SER A 393 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" CA SER B 86 " pdb=" C SER B 86 " ideal model delta sigma weight residual 1.523 1.476 0.048 1.34e-02 5.57e+03 1.26e+01 bond pdb=" C SER A 396 " pdb=" O SER A 396 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.26e+01 ... (remaining 5587 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 119 105.52 - 112.66: 2878 112.66 - 119.79: 2008 119.79 - 126.93: 2527 126.93 - 134.06: 83 Bond angle restraints: 7615 Sorted by residual: angle pdb=" N CYS A 355 " pdb=" CA CYS A 355 " pdb=" C CYS A 355 " ideal model delta sigma weight residual 112.88 121.38 -8.50 1.29e+00 6.01e-01 4.34e+01 angle pdb=" N PRO A 465 " pdb=" CA PRO A 465 " pdb=" C PRO A 465 " ideal model delta sigma weight residual 110.70 117.64 -6.94 1.22e+00 6.72e-01 3.24e+01 angle pdb=" N SER A 77 " pdb=" CA SER A 77 " pdb=" C SER A 77 " ideal model delta sigma weight residual 111.07 117.15 -6.08 1.07e+00 8.73e-01 3.23e+01 angle pdb=" N LEU B 87 " pdb=" CA LEU B 87 " pdb=" C LEU B 87 " ideal model delta sigma weight residual 110.50 118.42 -7.92 1.41e+00 5.03e-01 3.15e+01 angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" C ALA A 464 " ideal model delta sigma weight residual 109.81 120.50 -10.69 2.21e+00 2.05e-01 2.34e+01 ... (remaining 7610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 2901 15.94 - 31.88: 318 31.88 - 47.81: 74 47.81 - 63.75: 7 63.75 - 79.69: 6 Dihedral angle restraints: 3306 sinusoidal: 1288 harmonic: 2018 Sorted by residual: dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 159.85 -66.85 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CA ARG B 106 " pdb=" C ARG B 106 " pdb=" N TYR B 107 " pdb=" CA TYR B 107 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" N CYS A 355 " pdb=" C CYS A 355 " pdb=" CA CYS A 355 " pdb=" CB CYS A 355 " ideal model delta harmonic sigma weight residual 122.80 135.15 -12.35 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 3303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 848 0.122 - 0.243: 43 0.243 - 0.365: 3 0.365 - 0.487: 1 0.487 - 0.608: 1 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA CYS A 355 " pdb=" N CYS A 355 " pdb=" C CYS A 355 " pdb=" CB CYS A 355 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" CA LYS A 358 " pdb=" N LYS A 358 " pdb=" C LYS A 358 " pdb=" CB LYS A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA LEU B 87 " pdb=" N LEU B 87 " pdb=" C LEU B 87 " pdb=" CB LEU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 893 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 330 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 331 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 394 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU A 394 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 394 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 395 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " 0.053 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO A 466 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " 0.044 5.00e-02 4.00e+02 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 721 2.75 - 3.29: 4711 3.29 - 3.82: 7947 3.82 - 4.36: 8810 4.36 - 4.90: 16705 Nonbonded interactions: 38894 Sorted by model distance: nonbonded pdb=" O SER B 86 " pdb=" OG SER B 86 " model vdw 2.210 2.440 nonbonded pdb=" O SER A 64 " pdb=" OG SER A 64 " model vdw 2.359 2.440 nonbonded pdb=" O SER B 58 " pdb=" OG SER B 58 " model vdw 2.361 2.440 nonbonded pdb=" ND2 ASN A 25 " pdb=" OD1 ASN A 376 " model vdw 2.371 2.520 nonbonded pdb=" NH2 ARG A 558 " pdb=" O GLU A 568 " model vdw 2.375 2.520 ... (remaining 38889 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=0.70 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.130 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.740 Find NCS groups from input model: 0.150 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.009 0.095 5592 Z= 0.556 Angle : 1.006 10.688 7615 Z= 0.582 Chirality : 0.065 0.608 896 Planarity : 0.008 0.084 923 Dihedral : 13.721 79.687 2001 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.74 % Allowed : 10.42 % Favored : 87.85 % Cbeta Deviations : 0.31 % 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: -4.25 (0.25), residues: 694 helix: -2.22 (0.21), residues: 381 sheet: -3.16 (0.61), residues: 54 loop : -3.51 (0.31), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 276 HIS 0.005 0.002 HIS A 20 PHE 0.026 0.002 PHE A 534 TYR 0.012 0.002 TYR A 526 ARG 0.006 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.645 Fit side-chains REVERT: A 192 THR cc_start: 0.8278 (t) cc_final: 0.8012 (p) REVERT: A 252 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7502 (mm-40) REVERT: A 254 LYS cc_start: 0.8696 (pttm) cc_final: 0.8240 (ptpp) REVERT: A 374 MET cc_start: 0.8388 (mmm) cc_final: 0.7879 (mmt) REVERT: B 35 LYS cc_start: 0.8125 (tttt) cc_final: 0.7657 (tptp) REVERT: B 70 THR cc_start: 0.8652 (m) cc_final: 0.8290 (p) outliers start: 10 outliers final: 5 residues processed: 118 average time/residue: 0.2138 time to fit residues: 31.5006 Evaluate side-chains 86 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 89 PRO Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5592 Z= 0.223 Angle : 0.659 11.811 7615 Z= 0.344 Chirality : 0.043 0.153 896 Planarity : 0.007 0.081 923 Dihedral : 7.261 56.462 834 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.95 % Allowed : 14.58 % Favored : 82.47 % 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: -2.18 (0.31), residues: 694 helix: -0.18 (0.27), residues: 380 sheet: -2.27 (0.73), residues: 49 loop : -3.21 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.004 0.001 HIS A 20 PHE 0.015 0.001 PHE A 534 TYR 0.019 0.002 TYR A 290 ARG 0.007 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.617 Fit side-chains REVERT: A 254 LYS cc_start: 0.9041 (pttm) cc_final: 0.8715 (pttm) REVERT: A 285 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 382 MET cc_start: 0.6731 (mmm) cc_final: 0.6495 (mmt) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.2004 time to fit residues: 23.2469 Evaluate side-chains 75 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.0010 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5592 Z= 0.172 Angle : 0.554 7.120 7615 Z= 0.292 Chirality : 0.041 0.156 896 Planarity : 0.005 0.053 923 Dihedral : 6.023 43.208 829 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % Favored : 79.17 % 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: -1.24 (0.32), residues: 694 helix: 0.77 (0.29), residues: 375 sheet: -1.79 (0.77), residues: 49 loop : -3.03 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 68 HIS 0.007 0.001 HIS A 20 PHE 0.013 0.001 PHE A 534 TYR 0.010 0.001 TYR B 61 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.612 Fit side-chains REVERT: A 254 LYS cc_start: 0.9072 (pttm) cc_final: 0.8752 (pttm) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.1929 time to fit residues: 20.5182 Evaluate side-chains 73 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.0000 chunk 6 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5592 Z= 0.140 Angle : 0.521 7.026 7615 Z= 0.272 Chirality : 0.039 0.134 896 Planarity : 0.005 0.046 923 Dihedral : 5.670 52.174 826 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.08 % Allowed : 18.40 % Favored : 79.51 % 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: -0.75 (0.33), residues: 694 helix: 1.14 (0.29), residues: 386 sheet: -1.54 (0.79), residues: 49 loop : -2.96 (0.32), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.010 0.001 PHE A 534 TYR 0.010 0.001 TYR B 61 ARG 0.009 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.663 Fit side-chains REVERT: A 254 LYS cc_start: 0.9130 (pttm) cc_final: 0.8843 (pttm) REVERT: A 374 MET cc_start: 0.8530 (mmm) cc_final: 0.8283 (mmt) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.2246 time to fit residues: 20.7857 Evaluate side-chains 66 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5592 Z= 0.190 Angle : 0.548 7.212 7615 Z= 0.289 Chirality : 0.041 0.144 896 Planarity : 0.004 0.046 923 Dihedral : 5.697 55.611 826 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.91 % Allowed : 19.97 % Favored : 78.12 % 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: -0.52 (0.34), residues: 694 helix: 1.24 (0.29), residues: 391 sheet: -1.33 (0.83), residues: 49 loop : -2.80 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.017 0.001 PHE A 534 TYR 0.010 0.001 TYR A 526 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.629 Fit side-chains REVERT: A 374 MET cc_start: 0.8616 (mmm) cc_final: 0.8371 (mmt) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.2140 time to fit residues: 20.1201 Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8129 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5592 Z= 0.182 Angle : 0.539 7.270 7615 Z= 0.281 Chirality : 0.040 0.140 896 Planarity : 0.004 0.045 923 Dihedral : 4.712 38.253 826 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.08 % Allowed : 20.83 % Favored : 77.08 % 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: -0.41 (0.34), residues: 694 helix: 1.27 (0.29), residues: 395 sheet: -1.34 (0.82), residues: 49 loop : -2.70 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.014 0.001 PHE A 534 TYR 0.012 0.001 TYR B 61 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.660 Fit side-chains REVERT: A 237 MET cc_start: 0.9063 (mmm) cc_final: 0.8863 (mmt) REVERT: A 374 MET cc_start: 0.8611 (mmm) cc_final: 0.8348 (mmt) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.2240 time to fit residues: 20.9271 Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 20 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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: 0.8067 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5592 Z= 0.133 Angle : 0.512 7.144 7615 Z= 0.266 Chirality : 0.039 0.131 896 Planarity : 0.004 0.042 923 Dihedral : 4.358 28.004 826 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.74 % Allowed : 21.70 % Favored : 76.56 % 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: -0.13 (0.34), residues: 694 helix: 1.51 (0.28), residues: 394 sheet: -1.27 (0.83), residues: 49 loop : -2.56 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.009 0.001 PHE A 534 TYR 0.011 0.001 TYR B 61 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.628 Fit side-chains REVERT: A 237 MET cc_start: 0.9087 (mmm) cc_final: 0.8801 (mmt) REVERT: A 374 MET cc_start: 0.8584 (mmm) cc_final: 0.8349 (mmt) outliers start: 10 outliers final: 10 residues processed: 76 average time/residue: 0.2135 time to fit residues: 20.5209 Evaluate side-chains 73 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 63 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5592 Z= 0.167 Angle : 0.531 7.186 7615 Z= 0.277 Chirality : 0.039 0.132 896 Planarity : 0.004 0.043 923 Dihedral : 4.313 26.853 826 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.60 % Allowed : 21.18 % Favored : 76.22 % 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: -0.08 (0.34), residues: 694 helix: 1.67 (0.29), residues: 387 sheet: -1.26 (0.83), residues: 49 loop : -2.64 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.012 0.001 PHE A 534 TYR 0.010 0.001 TYR B 61 ARG 0.007 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.578 Fit side-chains REVERT: A 87 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 237 MET cc_start: 0.9079 (mmm) cc_final: 0.8824 (mmt) REVERT: A 374 MET cc_start: 0.8609 (mmm) cc_final: 0.8370 (mmt) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.1867 time to fit residues: 18.2315 Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5592 Z= 0.184 Angle : 0.538 7.274 7615 Z= 0.281 Chirality : 0.040 0.138 896 Planarity : 0.004 0.043 923 Dihedral : 4.340 26.211 826 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.43 % Allowed : 22.05 % Favored : 75.52 % 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: -0.06 (0.34), residues: 694 helix: 1.69 (0.28), residues: 387 sheet: -1.23 (0.83), residues: 49 loop : -2.64 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.007 0.001 HIS A 20 PHE 0.014 0.001 PHE A 534 TYR 0.010 0.001 TYR B 61 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.572 Fit side-chains REVERT: A 87 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7857 (mp) REVERT: A 374 MET cc_start: 0.8623 (mmm) cc_final: 0.8374 (mmt) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.1950 time to fit residues: 17.5732 Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5592 Z= 0.161 Angle : 0.518 7.235 7615 Z= 0.270 Chirality : 0.039 0.134 896 Planarity : 0.004 0.043 923 Dihedral : 4.251 26.174 826 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.43 % Allowed : 22.22 % Favored : 75.35 % 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: 0.02 (0.34), residues: 694 helix: 1.75 (0.29), residues: 387 sheet: -1.14 (0.83), residues: 49 loop : -2.62 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.012 0.001 PHE A 534 TYR 0.013 0.001 TYR B 61 ARG 0.006 0.000 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.556 Fit side-chains REVERT: A 87 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 374 MET cc_start: 0.8605 (mmm) cc_final: 0.8367 (mmt) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.1989 time to fit residues: 18.2338 Evaluate side-chains 68 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.0060 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.127727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098310 restraints weight = 6879.159| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.83 r_work: 0.3009 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5592 Z= 0.139 Angle : 0.502 7.155 7615 Z= 0.262 Chirality : 0.039 0.129 896 Planarity : 0.004 0.042 923 Dihedral : 4.137 26.301 826 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.43 % Allowed : 21.88 % Favored : 75.69 % 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: 0.19 (0.34), residues: 694 helix: 1.88 (0.29), residues: 386 sheet: -1.04 (0.83), residues: 49 loop : -2.52 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.006 0.001 HIS A 20 PHE 0.009 0.001 PHE A 534 TYR 0.012 0.001 TYR B 61 ARG 0.006 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.89 seconds wall clock time: 28 minutes 3.26 seconds (1683.26 seconds total)