Starting phenix.real_space_refine on Sat Dec 9 01:59:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/12_2023/7sch_25035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/12_2023/7sch_25035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/12_2023/7sch_25035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/12_2023/7sch_25035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/12_2023/7sch_25035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/12_2023/7sch_25035.pdb" } resolution = 3.1 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= 0.035 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 47 5.16 5 C 6250 2.51 5 N 1645 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4913 Classifications: {'peptide': 603} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 574} Chain breaks: 3 Chain: "B" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4759 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 548} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.31, per 1000 atoms: 0.55 Number of scatterers: 9711 At special positions: 0 Unit cell: (102.672, 87.768, 112.608, 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 47 16.00 O 1769 8.00 N 1645 7.00 C 6250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 637 " Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 39.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.689A pdb=" N LEU A 108 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.588A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.578A pdb=" N ALA A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.295A pdb=" N VAL A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.875A pdb=" N GLN A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.750A pdb=" N GLU A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.526A pdb=" N GLN A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.884A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.911A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.607A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.647A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.668A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.978A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.932A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.714A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.616A pdb=" N ARG B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.823A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.529A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.749A pdb=" N GLU B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.055A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.711A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.513A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 5.898A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 297 removed outlier: 8.240A pdb=" N VAL A 293 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR A 297 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY A 268 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET A 263 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 335 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 332 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 358 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 8.299A pdb=" N VAL A 537 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 513 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE A 539 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 515 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 516 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 484 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 481 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 564 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 483 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 removed outlier: 3.587A pdb=" N ARG A 605 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 726 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.380A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 7.924A pdb=" N LEU B 281 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.645A pdb=" N LEU B 485 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 512 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 487 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 535 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.565A pdb=" N LYS B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 843 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: 2.88 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2883 1.34 - 1.46: 1881 1.46 - 1.58: 5134 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 9972 Sorted by residual: bond pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.18e-02 7.18e+03 1.32e+01 bond pdb=" N PRO B 648 " pdb=" CA PRO B 648 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.51e+00 bond pdb=" N SER B 425 " pdb=" CA SER B 425 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.27e-02 6.20e+03 7.74e+00 bond pdb=" N LYS B 645 " pdb=" CA LYS B 645 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.91e+00 bond pdb=" N ARG B 649 " pdb=" CA ARG B 649 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.70e+00 ... (remaining 9967 not shown) Histogram of bond angle deviations from ideal: 96.31 - 103.93: 166 103.93 - 111.55: 4395 111.55 - 119.17: 3638 119.17 - 126.79: 5156 126.79 - 134.41: 191 Bond angle restraints: 13546 Sorted by residual: angle pdb=" N LYS B 645 " pdb=" CA LYS B 645 " pdb=" C LYS B 645 " ideal model delta sigma weight residual 110.55 105.46 5.09 1.35e+00 5.49e-01 1.42e+01 angle pdb=" CA LYS B 645 " pdb=" C LYS B 645 " pdb=" O LYS B 645 " ideal model delta sigma weight residual 121.81 117.49 4.32 1.18e+00 7.18e-01 1.34e+01 angle pdb=" CA LYS B 645 " pdb=" C LYS B 645 " pdb=" N VAL B 646 " ideal model delta sigma weight residual 115.27 119.65 -4.38 1.30e+00 5.92e-01 1.14e+01 angle pdb=" C TRP B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 122.73 117.40 5.33 1.61e+00 3.86e-01 1.10e+01 angle pdb=" N ASN B 430 " pdb=" CA ASN B 430 " pdb=" C ASN B 430 " ideal model delta sigma weight residual 112.72 116.33 -3.61 1.14e+00 7.69e-01 1.00e+01 ... (remaining 13541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5540 17.93 - 35.86: 381 35.86 - 53.78: 58 53.78 - 71.71: 8 71.71 - 89.64: 4 Dihedral angle restraints: 5991 sinusoidal: 2476 harmonic: 3515 Sorted by residual: dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual -86.00 -157.29 71.29 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual -86.00 -19.43 -66.57 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual 93.00 145.56 -52.56 1 1.00e+01 1.00e-02 3.76e+01 ... (remaining 5988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1205 0.055 - 0.110: 239 0.110 - 0.164: 29 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 1476 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU B 594 " pdb=" CB LEU B 594 " pdb=" CD1 LEU B 594 " pdb=" CD2 LEU B 594 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL B 646 " pdb=" CA VAL B 646 " pdb=" CG1 VAL B 646 " pdb=" CG2 VAL B 646 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1473 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 643 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C VAL B 643 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL B 643 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 644 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 248 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO B 249 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 559 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 560 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 560 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 560 " -0.025 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1264 2.75 - 3.29: 9392 3.29 - 3.83: 16123 3.83 - 4.36: 19715 4.36 - 4.90: 33561 Nonbonded interactions: 80055 Sorted by model distance: nonbonded pdb=" OG SER A 547 " pdb=" OD1 ASP A 647 " model vdw 2.218 2.440 nonbonded pdb=" ND2 ASN B 99 " pdb=" O LYS B 101 " model vdw 2.248 2.520 nonbonded pdb=" O TYR A 592 " pdb=" NZ LYS A 671 " model vdw 2.254 2.520 nonbonded pdb=" OG1 THR A 673 " pdb=" OD1 ASP A 725 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP A 382 " pdb=" NH2 ARG A 384 " model vdw 2.271 2.520 ... (remaining 80050 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: 0.780 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: 3.860 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 28.610 Find NCS groups from input model: 0.290 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.003 0.088 9972 Z= 0.208 Angle : 0.621 9.790 13546 Z= 0.340 Chirality : 0.045 0.274 1476 Planarity : 0.004 0.069 1725 Dihedral : 11.904 89.640 3692 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1174 helix: 0.94 (0.28), residues: 382 sheet: -0.48 (0.44), residues: 140 loop : -0.37 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 429 HIS 0.005 0.001 HIS B 88 PHE 0.011 0.001 PHE B 470 TYR 0.023 0.001 TYR B 582 ARG 0.006 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 318 average time/residue: 0.2551 time to fit residues: 107.8718 Evaluate side-chains 286 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1141 time to fit residues: 1.8656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 362 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN B 430 ASN B 550 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9972 Z= 0.168 Angle : 0.559 10.726 13546 Z= 0.282 Chirality : 0.043 0.138 1476 Planarity : 0.004 0.036 1725 Dihedral : 4.084 16.624 1349 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.97 % Allowed : 8.74 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.22 (0.25), residues: 1174 helix: 1.20 (0.28), residues: 381 sheet: -0.26 (0.45), residues: 137 loop : -0.34 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 556 HIS 0.007 0.001 HIS A 285 PHE 0.013 0.001 PHE A 598 TYR 0.030 0.001 TYR B 426 ARG 0.005 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 295 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 300 average time/residue: 0.2608 time to fit residues: 104.6191 Evaluate side-chains 304 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 293 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0974 time to fit residues: 3.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9972 Z= 0.218 Angle : 0.561 11.975 13546 Z= 0.283 Chirality : 0.043 0.142 1476 Planarity : 0.004 0.039 1725 Dihedral : 4.128 16.940 1349 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.32 % Allowed : 12.03 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.25), residues: 1174 helix: 1.41 (0.28), residues: 376 sheet: -0.09 (0.43), residues: 147 loop : -0.40 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 599 HIS 0.007 0.001 HIS A 285 PHE 0.011 0.001 PHE B 217 TYR 0.024 0.001 TYR B 426 ARG 0.007 0.000 ARG A 605 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 294 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 297 average time/residue: 0.2759 time to fit residues: 109.6559 Evaluate side-chains 290 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1454 time to fit residues: 3.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.4980 chunk 80 optimal weight: 0.0170 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 398 GLN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 328 GLN B 415 ASN B 550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9972 Z= 0.167 Angle : 0.537 9.905 13546 Z= 0.271 Chirality : 0.042 0.142 1476 Planarity : 0.004 0.041 1725 Dihedral : 4.033 16.360 1349 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.60 % Allowed : 13.82 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.46 (0.25), residues: 1174 helix: 1.50 (0.28), residues: 375 sheet: 0.14 (0.48), residues: 124 loop : -0.31 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.008 0.001 PHE A 410 TYR 0.022 0.001 TYR B 426 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 283 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 286 average time/residue: 0.2659 time to fit residues: 101.2957 Evaluate side-chains 290 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 279 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0999 time to fit residues: 3.5226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9972 Z= 0.194 Angle : 0.532 10.458 13546 Z= 0.269 Chirality : 0.042 0.143 1476 Planarity : 0.004 0.042 1725 Dihedral : 4.026 16.447 1349 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.22 % Allowed : 15.32 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.43 (0.25), residues: 1174 helix: 1.48 (0.28), residues: 379 sheet: 0.22 (0.48), residues: 124 loop : -0.37 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.008 0.001 PHE A 659 TYR 0.023 0.001 TYR B 426 ARG 0.004 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 293 average time/residue: 0.2640 time to fit residues: 103.2026 Evaluate side-chains 289 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 281 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0958 time to fit residues: 2.7903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.1980 chunk 102 optimal weight: 0.0770 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9972 Z= 0.182 Angle : 0.536 8.788 13546 Z= 0.269 Chirality : 0.042 0.153 1476 Planarity : 0.004 0.045 1725 Dihedral : 4.017 16.091 1349 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.22 % Allowed : 17.01 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.43 (0.25), residues: 1174 helix: 1.45 (0.28), residues: 379 sheet: 0.31 (0.48), residues: 124 loop : -0.38 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 599 HIS 0.005 0.001 HIS A 285 PHE 0.009 0.001 PHE A 659 TYR 0.027 0.001 TYR A 319 ARG 0.004 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 286 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 288 average time/residue: 0.2621 time to fit residues: 100.8626 Evaluate side-chains 292 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 283 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1596 time to fit residues: 3.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9972 Z= 0.173 Angle : 0.536 8.617 13546 Z= 0.271 Chirality : 0.042 0.144 1476 Planarity : 0.004 0.045 1725 Dihedral : 3.967 15.569 1349 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.94 % Allowed : 17.39 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.45 (0.25), residues: 1174 helix: 1.44 (0.28), residues: 380 sheet: 0.33 (0.48), residues: 124 loop : -0.35 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.009 0.001 PHE A 659 TYR 0.024 0.001 TYR A 319 ARG 0.004 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 289 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 291 average time/residue: 0.2569 time to fit residues: 100.7985 Evaluate side-chains 287 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 280 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0966 time to fit residues: 2.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.0270 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9972 Z= 0.216 Angle : 0.557 8.611 13546 Z= 0.280 Chirality : 0.043 0.144 1476 Planarity : 0.004 0.054 1725 Dihedral : 4.061 16.262 1349 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.41 % Allowed : 17.01 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.42 (0.25), residues: 1174 helix: 1.43 (0.28), residues: 379 sheet: 0.13 (0.46), residues: 136 loop : -0.33 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.017 0.001 PHE B 317 TYR 0.023 0.001 TYR B 582 ARG 0.006 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 272 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 278 average time/residue: 0.2641 time to fit residues: 98.3989 Evaluate side-chains 277 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 269 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1010 time to fit residues: 3.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.0670 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 69 optimal weight: 0.0980 chunk 112 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 194 ASN A 362 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9972 Z= 0.174 Angle : 0.562 8.464 13546 Z= 0.283 Chirality : 0.043 0.144 1476 Planarity : 0.004 0.046 1725 Dihedral : 3.974 15.353 1349 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.66 % Allowed : 18.61 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.43 (0.25), residues: 1174 helix: 1.43 (0.28), residues: 379 sheet: 0.14 (0.46), residues: 136 loop : -0.32 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.009 0.001 PHE B 317 TYR 0.024 0.001 TYR B 582 ARG 0.004 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 279 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 282 average time/residue: 0.2424 time to fit residues: 91.9743 Evaluate side-chains 270 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1053 time to fit residues: 2.1006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 0.0040 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 chunk 99 optimal weight: 0.0570 overall best weight: 0.0418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9972 Z= 0.140 Angle : 0.558 10.002 13546 Z= 0.279 Chirality : 0.042 0.137 1476 Planarity : 0.004 0.044 1725 Dihedral : 3.798 14.161 1349 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.47 % Allowed : 18.98 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.51 (0.25), residues: 1174 helix: 1.61 (0.28), residues: 374 sheet: 0.23 (0.47), residues: 138 loop : -0.35 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 599 HIS 0.007 0.001 HIS B 571 PHE 0.016 0.001 PHE A 480 TYR 0.023 0.001 TYR B 582 ARG 0.006 0.000 ARG B 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 275 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 277 average time/residue: 0.2444 time to fit residues: 91.4717 Evaluate side-chains 278 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 275 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1134 time to fit residues: 2.0911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.0000 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 96 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123271 restraints weight = 13546.443| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.17 r_work: 0.3400 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9972 Z= 0.153 Angle : 0.560 8.447 13546 Z= 0.280 Chirality : 0.042 0.136 1476 Planarity : 0.004 0.044 1725 Dihedral : 3.769 14.146 1349 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.85 % Allowed : 19.08 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1174 helix: 1.48 (0.28), residues: 380 sheet: 0.31 (0.47), residues: 136 loop : -0.28 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 599 HIS 0.005 0.001 HIS B 571 PHE 0.023 0.001 PHE A 480 TYR 0.021 0.001 TYR A 319 ARG 0.006 0.000 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.10 seconds wall clock time: 51 minutes 16.09 seconds (3076.09 seconds total)