Starting phenix.real_space_refine on Wed Feb 14 16:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2024/7sch_25035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2024/7sch_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_25035/02_2024/7sch_25035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2024/7sch_25035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2024/7sch_25035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sch_25035/02_2024/7sch_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-dev-5238/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: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.57, per 1000 atoms: 0.57 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: 3.86 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: 1.12 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: 2.86 Time building geometry restraints manager: 4.17 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 - 21.80: 5665 21.80 - 43.60: 306 43.60 - 65.40: 22 65.40 - 87.20: 12 87.20 - 109.00: 5 Dihedral angle restraints: 6010 sinusoidal: 2495 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 6007 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: 1.090 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: 4.000 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- 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 : 12.800 108.998 3711 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 : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7225 (mpp) cc_final: 0.6882 (mpp) REVERT: B 176 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6539 (tm-30) REVERT: B 607 LEU cc_start: 0.7947 (mt) cc_final: 0.7684 (mt) outliers start: 2 outliers final: 2 residues processed: 318 average time/residue: 0.2442 time to fit residues: 103.6592 Evaluate side-chains 287 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN 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: 0.0980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.2590 ------------------------------------------------------------------------------- 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 ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9972 Z= 0.152 Angle : 0.554 11.124 13546 Z= 0.276 Chirality : 0.043 0.137 1476 Planarity : 0.004 0.037 1725 Dihedral : 6.536 67.172 1372 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.97 % Allowed : 8.93 % Favored : 89.10 % 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: 0.24 (0.25), residues: 1174 helix: 1.22 (0.28), residues: 381 sheet: -0.25 (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 0.012 0.001 PHE A 598 TYR 0.015 0.001 TYR B 582 ARG 0.005 0.000 ARG B 383 *********************** 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 318 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 297 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7229 (mpp) cc_final: 0.6887 (mpp) REVERT: A 706 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7228 (m-40) REVERT: B 145 ASP cc_start: 0.7237 (m-30) cc_final: 0.7020 (m-30) REVERT: B 154 VAL cc_start: 0.8187 (m) cc_final: 0.7959 (t) REVERT: B 176 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6437 (tm-30) REVERT: B 426 TYR cc_start: 0.3601 (OUTLIER) cc_final: 0.2984 (p90) REVERT: B 470 PHE cc_start: 0.7830 (m-80) cc_final: 0.7616 (m-80) REVERT: B 583 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6206 (tm-30) REVERT: B 607 LEU cc_start: 0.7946 (mt) cc_final: 0.7650 (mt) REVERT: B 612 MET cc_start: 0.7252 (tpp) cc_final: 0.6803 (tpp) outliers start: 21 outliers final: 11 residues processed: 302 average time/residue: 0.2555 time to fit residues: 102.8635 Evaluate side-chains 298 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 285 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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: 0.7214 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9972 Z= 0.268 Angle : 0.568 7.731 13546 Z= 0.288 Chirality : 0.044 0.145 1476 Planarity : 0.004 0.042 1725 Dihedral : 5.879 52.322 1372 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.26 % Allowed : 11.37 % Favored : 86.37 % 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: 0.30 (0.25), residues: 1174 helix: 1.38 (0.28), residues: 376 sheet: -0.06 (0.43), residues: 146 loop : -0.40 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 599 HIS 0.008 0.001 HIS A 285 PHE 0.012 0.002 PHE B 217 TYR 0.017 0.001 TYR A 608 ARG 0.006 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 314 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 290 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7475 (t0) cc_final: 0.7262 (t70) REVERT: A 359 MET cc_start: 0.7301 (mpp) cc_final: 0.6921 (mpp) REVERT: A 609 THR cc_start: 0.7598 (m) cc_final: 0.7326 (p) REVERT: B 106 VAL cc_start: 0.8430 (m) cc_final: 0.8180 (t) REVERT: B 176 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6466 (tm-30) REVERT: B 452 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6474 (mm-40) REVERT: B 539 ASP cc_start: 0.6217 (p0) cc_final: 0.5992 (p0) REVERT: B 583 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6273 (tm-30) REVERT: B 607 LEU cc_start: 0.7979 (mt) cc_final: 0.7666 (mt) REVERT: B 612 MET cc_start: 0.7278 (tpp) cc_final: 0.6942 (tpp) outliers start: 24 outliers final: 15 residues processed: 298 average time/residue: 0.2645 time to fit residues: 104.9120 Evaluate side-chains 296 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 280 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN 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 B 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1610 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= 0.210 Angle : 0.546 8.359 13546 Z= 0.275 Chirality : 0.043 0.145 1476 Planarity : 0.004 0.044 1725 Dihedral : 5.338 43.338 1372 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.20 % Allowed : 12.59 % Favored : 84.21 % 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: 0.40 (0.25), residues: 1174 helix: 1.45 (0.28), residues: 375 sheet: 0.03 (0.46), residues: 134 loop : -0.33 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 599 HIS 0.007 0.001 HIS A 285 PHE 0.009 0.001 PHE B 217 TYR 0.016 0.001 TYR A 608 ARG 0.004 0.000 ARG B 128 *********************** 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 317 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 283 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7283 (mpp) cc_final: 0.6840 (mpp) REVERT: A 609 THR cc_start: 0.7528 (m) cc_final: 0.7236 (p) REVERT: B 176 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6401 (tm-30) REVERT: B 415 ASN cc_start: 0.8628 (t0) cc_final: 0.8415 (t0) REVERT: B 539 ASP cc_start: 0.6150 (p0) cc_final: 0.5852 (p0) REVERT: B 583 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6318 (tm-30) REVERT: B 607 LEU cc_start: 0.7983 (mt) cc_final: 0.7661 (mt) REVERT: B 612 MET cc_start: 0.7360 (tpp) cc_final: 0.7030 (tpp) outliers start: 34 outliers final: 24 residues processed: 295 average time/residue: 0.2569 time to fit residues: 100.7536 Evaluate side-chains 302 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9972 Z= 0.224 Angle : 0.545 8.868 13546 Z= 0.276 Chirality : 0.043 0.145 1476 Planarity : 0.004 0.043 1725 Dihedral : 5.153 41.018 1372 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.91 % Allowed : 13.72 % Favored : 83.36 % 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: 0.39 (0.25), residues: 1174 helix: 1.48 (0.28), residues: 375 sheet: 0.02 (0.45), residues: 136 loop : -0.36 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 599 HIS 0.007 0.001 HIS A 285 PHE 0.009 0.001 PHE A 659 TYR 0.016 0.001 TYR A 608 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 314 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 283 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8355 (m) REVERT: A 359 MET cc_start: 0.7272 (mpp) cc_final: 0.6822 (mpp) REVERT: A 609 THR cc_start: 0.7511 (m) cc_final: 0.7196 (p) REVERT: B 176 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6403 (tm-30) REVERT: B 539 ASP cc_start: 0.6184 (p0) cc_final: 0.5872 (p0) REVERT: B 583 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6302 (tm-30) REVERT: B 607 LEU cc_start: 0.7979 (mt) cc_final: 0.7672 (mt) REVERT: B 612 MET cc_start: 0.7385 (tpp) cc_final: 0.7056 (tpp) outliers start: 31 outliers final: 26 residues processed: 291 average time/residue: 0.2623 time to fit residues: 102.2567 Evaluate side-chains 306 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 388 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 415 ASN B 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 0.043 9972 Z= 0.196 Angle : 0.538 7.823 13546 Z= 0.271 Chirality : 0.043 0.144 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.903 38.249 1372 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.29 % Allowed : 14.19 % Favored : 82.52 % 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: 0.38 (0.25), residues: 1174 helix: 1.45 (0.28), residues: 379 sheet: 0.08 (0.45), residues: 136 loop : -0.38 (0.25), residues: 659 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 0.009 0.001 PHE A 659 TYR 0.016 0.001 TYR A 608 ARG 0.005 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 322 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8310 (m) REVERT: A 359 MET cc_start: 0.7274 (mpp) cc_final: 0.6820 (mpp) REVERT: A 609 THR cc_start: 0.7462 (m) cc_final: 0.7186 (p) REVERT: B 176 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6413 (tm-30) REVERT: B 539 ASP cc_start: 0.6197 (p0) cc_final: 0.5873 (p0) REVERT: B 607 LEU cc_start: 0.7976 (mt) cc_final: 0.7675 (mt) REVERT: B 612 MET cc_start: 0.7368 (tpp) cc_final: 0.7049 (tpp) REVERT: B 627 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5659 (mp0) outliers start: 35 outliers final: 22 residues processed: 301 average time/residue: 0.2552 time to fit residues: 103.0737 Evaluate side-chains 304 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 706 ASN B 415 ASN B 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9972 Z= 0.440 Angle : 0.645 8.035 13546 Z= 0.331 Chirality : 0.048 0.168 1476 Planarity : 0.005 0.044 1725 Dihedral : 5.686 40.304 1372 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.85 % Allowed : 14.47 % 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: -0.02 (0.25), residues: 1174 helix: 0.86 (0.27), residues: 391 sheet: -0.12 (0.45), residues: 132 loop : -0.48 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 599 HIS 0.010 0.001 HIS A 285 PHE 0.018 0.002 PHE A 333 TYR 0.021 0.002 TYR B 582 ARG 0.007 0.001 ARG A 440 *********************** 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 326 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 285 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7815 (t70) cc_final: 0.7580 (t70) REVERT: A 160 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8359 (m) REVERT: A 359 MET cc_start: 0.7238 (mpp) cc_final: 0.6824 (mpp) REVERT: A 362 ASN cc_start: 0.7522 (m110) cc_final: 0.7139 (m-40) REVERT: A 382 ASP cc_start: 0.6986 (t0) cc_final: 0.6676 (t0) REVERT: A 609 THR cc_start: 0.7633 (m) cc_final: 0.7359 (p) REVERT: B 176 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6484 (tm-30) REVERT: B 539 ASP cc_start: 0.6376 (p0) cc_final: 0.6072 (p0) REVERT: B 569 ARG cc_start: 0.6756 (mpt180) cc_final: 0.6401 (mpt180) REVERT: B 607 LEU cc_start: 0.8028 (mt) cc_final: 0.7721 (mt) outliers start: 41 outliers final: 27 residues processed: 299 average time/residue: 0.2586 time to fit residues: 104.1217 Evaluate side-chains 307 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 279 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 300 HIS A 376 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN B 328 GLN B 415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9972 Z= 0.206 Angle : 0.582 10.669 13546 Z= 0.292 Chirality : 0.044 0.153 1476 Planarity : 0.004 0.045 1725 Dihedral : 5.099 31.354 1370 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.63 % Allowed : 16.35 % Favored : 81.02 % 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: 0.16 (0.25), residues: 1174 helix: 1.16 (0.28), residues: 384 sheet: -0.04 (0.47), residues: 127 loop : -0.45 (0.25), residues: 663 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 0.017 0.001 TYR A 608 ARG 0.007 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 312 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7753 (t70) cc_final: 0.7520 (t70) REVERT: A 160 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8290 (m) REVERT: A 359 MET cc_start: 0.7165 (mpp) cc_final: 0.6718 (mpp) REVERT: A 609 THR cc_start: 0.7545 (m) cc_final: 0.7252 (p) REVERT: B 176 GLN cc_start: 0.7101 (tm-30) cc_final: 0.6451 (tm-30) REVERT: B 539 ASP cc_start: 0.6328 (p0) cc_final: 0.6000 (p0) REVERT: B 607 LEU cc_start: 0.8014 (mt) cc_final: 0.7708 (mt) outliers start: 28 outliers final: 22 residues processed: 290 average time/residue: 0.2472 time to fit residues: 96.1745 Evaluate side-chains 301 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 278 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 376 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 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: 0.7214 moved from start: 0.2147 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= 0.204 Angle : 0.565 8.463 13546 Z= 0.286 Chirality : 0.044 0.148 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.820 25.688 1370 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.63 % Allowed : 16.92 % Favored : 80.45 % 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: 0.32 (0.25), residues: 1174 helix: 1.37 (0.28), residues: 379 sheet: 0.01 (0.47), residues: 127 loop : -0.39 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.010 0.001 PHE B 317 TYR 0.022 0.001 TYR B 582 ARG 0.007 0.000 ARG B 182 *********************** 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 306 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 278 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7754 (t70) cc_final: 0.7518 (t70) REVERT: A 160 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8281 (m) REVERT: A 359 MET cc_start: 0.7150 (mpp) cc_final: 0.6764 (mpp) REVERT: A 577 PHE cc_start: 0.7465 (t80) cc_final: 0.7190 (t80) REVERT: A 609 THR cc_start: 0.7505 (m) cc_final: 0.7207 (p) REVERT: B 176 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6406 (tm-30) REVERT: B 539 ASP cc_start: 0.6282 (p0) cc_final: 0.5948 (p0) REVERT: B 607 LEU cc_start: 0.8007 (mt) cc_final: 0.7692 (mt) outliers start: 28 outliers final: 23 residues processed: 286 average time/residue: 0.2527 time to fit residues: 96.6356 Evaluate side-chains 305 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 281 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 706 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2131 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= 0.199 Angle : 0.577 9.781 13546 Z= 0.289 Chirality : 0.043 0.146 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.591 22.008 1368 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.91 % Allowed : 17.58 % Favored : 79.51 % 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: 0.32 (0.25), residues: 1174 helix: 1.40 (0.28), residues: 379 sheet: 0.02 (0.48), residues: 127 loop : -0.41 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.011 0.001 PHE B 317 TYR 0.016 0.001 TYR A 608 ARG 0.007 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 310 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7773 (t70) cc_final: 0.7538 (t70) REVERT: A 160 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8273 (m) REVERT: A 359 MET cc_start: 0.7152 (mpp) cc_final: 0.6748 (mpp) REVERT: A 609 THR cc_start: 0.7489 (m) cc_final: 0.7195 (p) REVERT: B 176 GLN cc_start: 0.6998 (tm-30) cc_final: 0.6411 (tm-30) REVERT: B 539 ASP cc_start: 0.6277 (p0) cc_final: 0.5900 (p0) REVERT: B 607 LEU cc_start: 0.8015 (mt) cc_final: 0.7724 (mt) REVERT: B 620 VAL cc_start: 0.7185 (t) cc_final: 0.6937 (t) REVERT: B 627 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.5464 (mp0) outliers start: 31 outliers final: 25 residues processed: 288 average time/residue: 0.2552 time to fit residues: 99.4138 Evaluate side-chains 301 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 274 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 706 ASN B 415 ASN B 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119813 restraints weight = 13563.384| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.14 r_work: 0.3369 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9972 Z= 0.198 Angle : 0.565 8.575 13546 Z= 0.284 Chirality : 0.043 0.147 1476 Planarity : 0.004 0.044 1725 Dihedral : 4.488 22.306 1368 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.73 % Allowed : 17.58 % Favored : 79.70 % 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: 0.36 (0.25), residues: 1174 helix: 1.41 (0.28), residues: 379 sheet: 0.23 (0.48), residues: 124 loop : -0.42 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 599 HIS 0.006 0.001 HIS A 285 PHE 0.017 0.001 PHE A 266 TYR 0.016 0.001 TYR A 608 ARG 0.007 0.000 ARG B 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.17 seconds wall clock time: 51 minutes 39.38 seconds (3099.38 seconds total)