Starting phenix.real_space_refine on Wed Sep 25 11:29:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wla_32579/09_2024/7wla_32579.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wla_32579/09_2024/7wla_32579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wla_32579/09_2024/7wla_32579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wla_32579/09_2024/7wla_32579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wla_32579/09_2024/7wla_32579.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wla_32579/09_2024/7wla_32579.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 42 5.16 5 C 6653 2.51 5 N 1687 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10193 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 6.21, per 1000 atoms: 0.61 Number of scatterers: 10193 At special positions: 0 Unit cell: (85.772, 127.612, 123.428, 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 42 16.00 O 1811 8.00 N 1687 7.00 C 6653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 6 sheets defined 64.3% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.765A pdb=" N GLN A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.851A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 5.125A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.967A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.958A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.699A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.909A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.598A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.673A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.582A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.560A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.608A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.844A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.728A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.653A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.642A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.738A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.547A pdb=" N VAL A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.770A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.908A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.752A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.622A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.878A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 109 removed outlier: 3.540A pdb=" N SER B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.546A pdb=" N LEU B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.716A pdb=" N LEU B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 204 removed outlier: 3.839A pdb=" N GLY B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 225 through 240 removed outlier: 4.136A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.651A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 370 removed outlier: 4.130A pdb=" N ALA B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.525A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.578A pdb=" N GLU B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.525A pdb=" N LEU B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.651A pdb=" N ALA B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 466 through 475 removed outlier: 3.885A pdb=" N ARG B 470 " --> pdb=" O CYS B 466 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.552A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 removed outlier: 3.690A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 575 through 595 removed outlier: 3.590A pdb=" N ASN B 579 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.602A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 4.177A pdb=" N GLU B 701 " --> pdb=" O ASP B 697 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.575A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.724A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.743A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 548 removed outlier: 6.375A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1593 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: 2.74 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 2247 1.46 - 1.58: 4872 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10395 Sorted by residual: bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.64e-01 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.45e-01 bond pdb=" C GLU B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.08e-01 bond pdb=" CA PHE A 122 " pdb=" C PHE A 122 " ideal model delta sigma weight residual 1.521 1.530 -0.009 1.14e-02 7.69e+03 6.08e-01 bond pdb=" N PRO B 337 " pdb=" CA PRO B 337 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 5.47e-01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13736 1.09 - 2.19: 298 2.19 - 3.28: 64 3.28 - 4.38: 19 4.38 - 5.47: 11 Bond angle restraints: 14128 Sorted by residual: angle pdb=" N ARG A 134 " pdb=" CA ARG A 134 " pdb=" C ARG A 134 " ideal model delta sigma weight residual 114.56 111.18 3.38 1.27e+00 6.20e-01 7.09e+00 angle pdb=" C PHE A 121 " pdb=" N PHE A 122 " pdb=" CA PHE A 122 " ideal model delta sigma weight residual 119.78 122.74 -2.96 1.24e+00 6.50e-01 5.72e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 113.74 -4.40 2.08e+00 2.31e-01 4.47e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 125.76 -3.79 1.80e+00 3.09e-01 4.43e+00 angle pdb=" C VAL A 328 " pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 121.54 125.51 -3.97 1.91e+00 2.74e-01 4.32e+00 ... (remaining 14123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5965 17.76 - 35.51: 179 35.51 - 53.27: 32 53.27 - 71.03: 0 71.03 - 88.79: 4 Dihedral angle restraints: 6180 sinusoidal: 2353 harmonic: 3827 Sorted by residual: dihedral pdb=" CB GLU B 259 " pdb=" CG GLU B 259 " pdb=" CD GLU B 259 " pdb=" OE1 GLU B 259 " ideal model delta sinusoidal sigma weight residual 0.00 86.02 -86.02 1 3.00e+01 1.11e-03 9.93e+00 dihedral pdb=" N ARG B 43 " pdb=" CA ARG B 43 " pdb=" CB ARG B 43 " pdb=" CG ARG B 43 " ideal model delta sinusoidal sigma weight residual -180.00 -128.09 -51.91 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" N ARG A 36 " pdb=" CA ARG A 36 " pdb=" CB ARG A 36 " pdb=" CG ARG A 36 " ideal model delta sinusoidal sigma weight residual -180.00 -128.25 -51.75 3 1.50e+01 4.44e-03 9.05e+00 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 957 0.026 - 0.052: 503 0.052 - 0.078: 177 0.078 - 0.104: 62 0.104 - 0.130: 17 Chirality restraints: 1716 Sorted by residual: chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 296 " pdb=" N ILE B 296 " pdb=" C ILE B 296 " pdb=" CB ILE B 296 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1713 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 75 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 76 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO A 553 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 654 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.018 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 705 2.74 - 3.28: 11232 3.28 - 3.82: 16750 3.82 - 4.36: 19648 4.36 - 4.90: 33038 Nonbonded interactions: 81373 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.225 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.242 3.120 ... (remaining 81368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 733) selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 595 or resid 651 through 733)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.480 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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: 33.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.002 0.043 10395 Z= 0.108 Angle : 0.445 5.469 14128 Z= 0.251 Chirality : 0.037 0.130 1716 Planarity : 0.003 0.043 1757 Dihedral : 8.816 88.787 3714 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.01 % Allowed : 5.52 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.19), residues: 1319 helix: -2.14 (0.15), residues: 815 sheet: -3.23 (0.68), residues: 30 loop : -3.49 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 83 HIS 0.001 0.000 HIS A 723 PHE 0.008 0.001 PHE A 555 TYR 0.005 0.001 TYR A 377 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 378 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.7066 (mmt90) REVERT: A 93 SER cc_start: 0.8253 (t) cc_final: 0.7920 (p) REVERT: A 122 PHE cc_start: 0.7110 (m-80) cc_final: 0.6612 (m-10) REVERT: A 195 LEU cc_start: 0.8547 (tp) cc_final: 0.7962 (tp) REVERT: A 199 ILE cc_start: 0.8218 (mt) cc_final: 0.7783 (mt) REVERT: A 206 LEU cc_start: 0.7834 (mt) cc_final: 0.7563 (mt) REVERT: A 213 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7195 (mtm-85) REVERT: A 231 VAL cc_start: 0.8650 (t) cc_final: 0.7990 (p) REVERT: A 235 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7666 (mm-40) REVERT: A 237 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7839 (ttpp) REVERT: A 238 ILE cc_start: 0.8539 (mt) cc_final: 0.8339 (tp) REVERT: A 260 ILE cc_start: 0.8844 (mt) cc_final: 0.8503 (tp) REVERT: A 272 PHE cc_start: 0.7779 (t80) cc_final: 0.7542 (t80) REVERT: A 280 ILE cc_start: 0.8880 (mt) cc_final: 0.8622 (tp) REVERT: A 286 LYS cc_start: 0.9159 (tppt) cc_final: 0.8796 (mmmm) REVERT: A 355 SER cc_start: 0.7752 (m) cc_final: 0.7495 (p) REVERT: A 384 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5550 (mm-30) REVERT: A 398 PHE cc_start: 0.7104 (m-80) cc_final: 0.6473 (m-10) REVERT: A 432 MET cc_start: 0.7370 (tpt) cc_final: 0.6650 (tpt) REVERT: A 473 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7502 (mtpt) REVERT: A 484 PHE cc_start: 0.8200 (t80) cc_final: 0.7761 (t80) REVERT: A 488 MET cc_start: 0.7136 (tpp) cc_final: 0.6686 (tpp) REVERT: A 512 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: A 546 LYS cc_start: 0.8240 (tptm) cc_final: 0.7857 (tptm) REVERT: A 564 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8221 (ttmm) REVERT: A 676 LEU cc_start: 0.8143 (mt) cc_final: 0.7890 (tp) REVERT: A 681 LYS cc_start: 0.7819 (tptt) cc_final: 0.6864 (tptt) REVERT: A 686 ILE cc_start: 0.8389 (pt) cc_final: 0.7896 (mm) REVERT: A 687 ASP cc_start: 0.6664 (t0) cc_final: 0.6180 (t0) REVERT: A 723 HIS cc_start: 0.7182 (t-170) cc_final: 0.6781 (t-90) REVERT: B 48 ASP cc_start: 0.6066 (p0) cc_final: 0.5755 (m-30) REVERT: B 118 TYR cc_start: 0.6964 (m-10) cc_final: 0.6603 (m-80) REVERT: B 137 SER cc_start: 0.8017 (t) cc_final: 0.7779 (p) REVERT: B 151 VAL cc_start: 0.7229 (m) cc_final: 0.6544 (p) REVERT: B 195 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5859 (tp) REVERT: B 199 ILE cc_start: 0.7579 (mp) cc_final: 0.7350 (mp) REVERT: B 231 VAL cc_start: 0.8453 (p) cc_final: 0.7928 (p) REVERT: B 232 LEU cc_start: 0.8370 (tp) cc_final: 0.8116 (tt) REVERT: B 235 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7169 (mm-40) REVERT: B 238 ILE cc_start: 0.8276 (tp) cc_final: 0.8035 (mt) REVERT: B 244 THR cc_start: 0.6562 (t) cc_final: 0.6358 (p) REVERT: B 251 LEU cc_start: 0.8599 (mm) cc_final: 0.6964 (mm) REVERT: B 255 TYR cc_start: 0.8066 (m-10) cc_final: 0.7567 (m-80) REVERT: B 260 ILE cc_start: 0.9166 (mt) cc_final: 0.8938 (tp) REVERT: B 262 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7242 (tp-100) REVERT: B 286 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7316 (ttmm) REVERT: B 293 LYS cc_start: 0.8550 (pptt) cc_final: 0.8230 (pptt) REVERT: B 309 ILE cc_start: 0.8849 (pt) cc_final: 0.8511 (mm) REVERT: B 320 GLU cc_start: 0.7648 (tp30) cc_final: 0.7428 (tp30) REVERT: B 371 TYR cc_start: 0.7105 (m-80) cc_final: 0.6726 (m-80) REVERT: B 375 HIS cc_start: 0.6369 (t-90) cc_final: 0.6065 (t-90) REVERT: B 426 ILE cc_start: 0.8357 (tp) cc_final: 0.8116 (pt) REVERT: B 473 LYS cc_start: 0.7903 (mttp) cc_final: 0.6765 (mttp) REVERT: B 475 ASN cc_start: 0.7784 (t0) cc_final: 0.7357 (t0) REVERT: B 483 VAL cc_start: 0.8716 (p) cc_final: 0.8459 (t) REVERT: B 487 ILE cc_start: 0.8462 (pt) cc_final: 0.8142 (mp) REVERT: B 488 MET cc_start: 0.6912 (tpp) cc_final: 0.5808 (tpp) REVERT: B 492 LEU cc_start: 0.8447 (mt) cc_final: 0.7570 (mt) REVERT: B 515 PHE cc_start: 0.8051 (m-80) cc_final: 0.7396 (m-80) REVERT: B 580 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7920 (mmmt) REVERT: B 583 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8374 (tttm) REVERT: B 677 ARG cc_start: 0.7336 (ttt180) cc_final: 0.7098 (ttp80) REVERT: B 682 GLU cc_start: 0.7805 (tp30) cc_final: 0.7533 (tp30) REVERT: B 695 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.4754 (mp) REVERT: B 701 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 705 GLN cc_start: 0.8165 (tt0) cc_final: 0.7898 (tt0) REVERT: B 706 CYS cc_start: 0.7461 (m) cc_final: 0.6640 (m) outliers start: 45 outliers final: 19 residues processed: 413 average time/residue: 0.2588 time to fit residues: 142.2819 Evaluate side-chains 332 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 114 GLN A 135 HIS A 246 ASN A 289 ASN A 413 GLN A 514 GLN A 519 ASN A 567 ASN A 728 HIS A 730 GLN A 732 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 324 ASN B 383 GLN B 446 GLN B 457 ASN B 474 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN B 689 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10395 Z= 0.257 Angle : 0.629 7.242 14128 Z= 0.330 Chirality : 0.043 0.212 1716 Planarity : 0.005 0.047 1757 Dihedral : 5.846 80.241 1458 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.81 % Allowed : 14.16 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1319 helix: -0.63 (0.17), residues: 812 sheet: -2.95 (0.80), residues: 32 loop : -2.96 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 83 HIS 0.004 0.001 HIS B 728 PHE 0.017 0.001 PHE B 229 TYR 0.022 0.002 TYR A 556 ARG 0.011 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 320 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7608 (tpp-160) cc_final: 0.7274 (mmt90) REVERT: A 93 SER cc_start: 0.8466 (t) cc_final: 0.8071 (p) REVERT: A 122 PHE cc_start: 0.7343 (m-80) cc_final: 0.6873 (m-10) REVERT: A 123 PRO cc_start: 0.8397 (Cg_exo) cc_final: 0.8168 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8551 (tp) cc_final: 0.7978 (tp) REVERT: A 199 ILE cc_start: 0.8217 (mt) cc_final: 0.7887 (mt) REVERT: A 231 VAL cc_start: 0.8710 (t) cc_final: 0.8002 (p) REVERT: A 235 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7622 (mm-40) REVERT: A 237 LYS cc_start: 0.8468 (ttpp) cc_final: 0.7997 (ttpp) REVERT: A 247 TYR cc_start: 0.7393 (m-10) cc_final: 0.6266 (m-10) REVERT: A 272 PHE cc_start: 0.7942 (t80) cc_final: 0.7381 (t80) REVERT: A 280 ILE cc_start: 0.8941 (mt) cc_final: 0.8730 (tp) REVERT: A 286 LYS cc_start: 0.9173 (tppt) cc_final: 0.8785 (mmmm) REVERT: A 355 SER cc_start: 0.7878 (m) cc_final: 0.7562 (p) REVERT: A 384 GLU cc_start: 0.6678 (mm-30) cc_final: 0.5956 (mm-30) REVERT: A 395 SER cc_start: 0.8609 (m) cc_final: 0.8109 (p) REVERT: A 398 PHE cc_start: 0.7166 (m-80) cc_final: 0.6423 (m-10) REVERT: A 432 MET cc_start: 0.7339 (tpt) cc_final: 0.6711 (tpt) REVERT: A 443 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7003 (pp20) REVERT: A 473 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7864 (mtpt) REVERT: A 484 PHE cc_start: 0.8258 (t80) cc_final: 0.7898 (t80) REVERT: A 488 MET cc_start: 0.7442 (tpp) cc_final: 0.6998 (tpp) REVERT: A 512 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8402 (mtm-85) REVERT: A 530 TYR cc_start: 0.7289 (m-80) cc_final: 0.7052 (m-80) REVERT: A 546 LYS cc_start: 0.8287 (tptm) cc_final: 0.7796 (tptm) REVERT: A 549 ARG cc_start: 0.6946 (ttt90) cc_final: 0.6269 (ttm-80) REVERT: A 556 TYR cc_start: 0.8131 (p90) cc_final: 0.7792 (p90) REVERT: A 560 ASP cc_start: 0.8105 (m-30) cc_final: 0.7891 (t0) REVERT: A 563 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7922 (ttmm) REVERT: A 662 CYS cc_start: 0.7908 (m) cc_final: 0.7444 (m) REVERT: A 686 ILE cc_start: 0.8639 (pt) cc_final: 0.8380 (mm) REVERT: A 687 ASP cc_start: 0.6842 (t0) cc_final: 0.6425 (t0) REVERT: A 723 HIS cc_start: 0.7102 (t-170) cc_final: 0.6872 (t-90) REVERT: B 29 GLU cc_start: 0.6801 (mp0) cc_final: 0.6560 (mp0) REVERT: B 118 TYR cc_start: 0.7142 (m-10) cc_final: 0.6771 (m-80) REVERT: B 195 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6223 (tp) REVERT: B 199 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7531 (mp) REVERT: B 207 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 230 GLN cc_start: 0.7930 (tp40) cc_final: 0.7352 (tm-30) REVERT: B 231 VAL cc_start: 0.8656 (p) cc_final: 0.7894 (p) REVERT: B 235 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7250 (mm-40) REVERT: B 236 LEU cc_start: 0.8053 (tp) cc_final: 0.7684 (tp) REVERT: B 237 LYS cc_start: 0.8261 (pttt) cc_final: 0.7749 (pmtt) REVERT: B 251 LEU cc_start: 0.8426 (mm) cc_final: 0.6752 (mm) REVERT: B 255 TYR cc_start: 0.8246 (m-10) cc_final: 0.7703 (m-80) REVERT: B 259 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 263 ASN cc_start: 0.7439 (t0) cc_final: 0.7004 (t0) REVERT: B 271 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7654 (p0) REVERT: B 286 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7928 (ttmm) REVERT: B 293 LYS cc_start: 0.8550 (pptt) cc_final: 0.8238 (tppt) REVERT: B 309 ILE cc_start: 0.8870 (pt) cc_final: 0.8643 (mm) REVERT: B 320 GLU cc_start: 0.7580 (tp30) cc_final: 0.7244 (tp30) REVERT: B 359 VAL cc_start: 0.7871 (p) cc_final: 0.7528 (m) REVERT: B 395 SER cc_start: 0.7585 (m) cc_final: 0.7052 (p) REVERT: B 487 ILE cc_start: 0.8590 (pt) cc_final: 0.8112 (mm) REVERT: B 488 MET cc_start: 0.7156 (tpp) cc_final: 0.5961 (tpp) REVERT: B 492 LEU cc_start: 0.8544 (mt) cc_final: 0.7728 (mt) REVERT: B 499 LEU cc_start: 0.8293 (tp) cc_final: 0.8033 (tp) REVERT: B 560 ASP cc_start: 0.7948 (p0) cc_final: 0.7706 (p0) REVERT: B 583 LYS cc_start: 0.8838 (tmmt) cc_final: 0.8511 (tttm) REVERT: B 677 ARG cc_start: 0.7508 (ttt180) cc_final: 0.7081 (ttp80) REVERT: B 682 GLU cc_start: 0.7959 (tp30) cc_final: 0.7737 (tp30) REVERT: B 701 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6967 (mm-30) REVERT: B 702 LYS cc_start: 0.7220 (tttm) cc_final: 0.6267 (tptp) REVERT: B 705 GLN cc_start: 0.8273 (tt0) cc_final: 0.8023 (tt0) REVERT: B 706 CYS cc_start: 0.7317 (m) cc_final: 0.5853 (m) outliers start: 54 outliers final: 33 residues processed: 350 average time/residue: 0.2560 time to fit residues: 121.4312 Evaluate side-chains 329 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 293 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS A 383 GLN A 567 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 324 ASN B 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10395 Z= 0.258 Angle : 0.641 8.176 14128 Z= 0.337 Chirality : 0.044 0.197 1716 Planarity : 0.005 0.053 1757 Dihedral : 5.836 82.329 1450 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.90 % Allowed : 17.19 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1319 helix: -0.19 (0.18), residues: 822 sheet: -2.47 (0.90), residues: 32 loop : -2.82 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.006 0.001 HIS A 728 PHE 0.023 0.001 PHE A 719 TYR 0.021 0.002 TYR A 556 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7680 (mm110) cc_final: 0.7392 (mm110) REVERT: A 36 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7293 (mmt90) REVERT: A 37 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: A 79 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7474 (mmt90) REVERT: A 93 SER cc_start: 0.8443 (t) cc_final: 0.8103 (p) REVERT: A 122 PHE cc_start: 0.7333 (m-80) cc_final: 0.6868 (m-10) REVERT: A 123 PRO cc_start: 0.8329 (Cg_exo) cc_final: 0.8096 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8605 (tp) cc_final: 0.8066 (tp) REVERT: A 199 ILE cc_start: 0.8236 (mt) cc_final: 0.7907 (mt) REVERT: A 231 VAL cc_start: 0.8725 (t) cc_final: 0.8167 (p) REVERT: A 235 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7746 (mm-40) REVERT: A 237 LYS cc_start: 0.8404 (ttpp) cc_final: 0.7987 (ttpp) REVERT: A 247 TYR cc_start: 0.7355 (m-10) cc_final: 0.6940 (m-10) REVERT: A 280 ILE cc_start: 0.8962 (mt) cc_final: 0.8739 (tp) REVERT: A 286 LYS cc_start: 0.9158 (tppt) cc_final: 0.8787 (mmmm) REVERT: A 371 TYR cc_start: 0.8104 (m-80) cc_final: 0.7795 (m-80) REVERT: A 383 GLN cc_start: 0.7544 (mt0) cc_final: 0.7328 (mt0) REVERT: A 384 GLU cc_start: 0.6607 (mm-30) cc_final: 0.5887 (mm-30) REVERT: A 395 SER cc_start: 0.8475 (m) cc_final: 0.8127 (p) REVERT: A 398 PHE cc_start: 0.7104 (m-80) cc_final: 0.6512 (m-80) REVERT: A 432 MET cc_start: 0.7385 (tpt) cc_final: 0.6690 (tpt) REVERT: A 443 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7131 (pp20) REVERT: A 447 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7974 (mttp) REVERT: A 473 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7931 (mtpt) REVERT: A 476 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8459 (mtpp) REVERT: A 478 ASP cc_start: 0.8314 (t0) cc_final: 0.7792 (t0) REVERT: A 484 PHE cc_start: 0.8282 (t80) cc_final: 0.7956 (t80) REVERT: A 488 MET cc_start: 0.7612 (tpp) cc_final: 0.7123 (tpp) REVERT: A 515 PHE cc_start: 0.8469 (m-80) cc_final: 0.8266 (m-10) REVERT: A 530 TYR cc_start: 0.7419 (m-80) cc_final: 0.7172 (m-80) REVERT: A 546 LYS cc_start: 0.8281 (tptm) cc_final: 0.7750 (tptm) REVERT: A 556 TYR cc_start: 0.8170 (p90) cc_final: 0.7891 (p90) REVERT: A 560 ASP cc_start: 0.8113 (m-30) cc_final: 0.7913 (t0) REVERT: A 563 LYS cc_start: 0.8337 (mmmt) cc_final: 0.7967 (ttmm) REVERT: A 662 CYS cc_start: 0.7992 (m) cc_final: 0.7670 (m) REVERT: A 679 ILE cc_start: 0.8509 (mt) cc_final: 0.8162 (mt) REVERT: A 686 ILE cc_start: 0.8731 (pt) cc_final: 0.8441 (mm) REVERT: A 687 ASP cc_start: 0.7007 (t0) cc_final: 0.6546 (t0) REVERT: A 698 ASP cc_start: 0.7633 (t0) cc_final: 0.7414 (t0) REVERT: A 715 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7228 (mmmm) REVERT: A 723 HIS cc_start: 0.7237 (t-170) cc_final: 0.7032 (t-90) REVERT: A 727 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.5700 (mm) REVERT: A 730 GLN cc_start: 0.8455 (mt0) cc_final: 0.7909 (mp10) REVERT: A 732 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7352 (mm-40) REVERT: B 29 GLU cc_start: 0.7129 (mp0) cc_final: 0.6821 (mp0) REVERT: B 103 MET cc_start: 0.5775 (mmt) cc_final: 0.5491 (mmt) REVERT: B 118 TYR cc_start: 0.7272 (m-10) cc_final: 0.6993 (m-80) REVERT: B 134 ARG cc_start: 0.6452 (mtt90) cc_final: 0.6203 (mtt90) REVERT: B 195 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6346 (tp) REVERT: B 199 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7632 (mp) REVERT: B 207 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 213 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7852 (mtm180) REVERT: B 230 GLN cc_start: 0.7965 (tp40) cc_final: 0.7416 (tm-30) REVERT: B 231 VAL cc_start: 0.8647 (p) cc_final: 0.7896 (p) REVERT: B 235 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7302 (mm-40) REVERT: B 236 LEU cc_start: 0.8129 (tp) cc_final: 0.7761 (tp) REVERT: B 237 LYS cc_start: 0.8320 (pttt) cc_final: 0.7903 (pttt) REVERT: B 251 LEU cc_start: 0.8471 (mm) cc_final: 0.6722 (mm) REVERT: B 255 TYR cc_start: 0.8234 (m-10) cc_final: 0.7648 (m-80) REVERT: B 259 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 263 ASN cc_start: 0.7631 (t0) cc_final: 0.7180 (t0) REVERT: B 271 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7321 (p0) REVERT: B 286 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7969 (mmmm) REVERT: B 293 LYS cc_start: 0.8566 (pptt) cc_final: 0.7983 (mmmm) REVERT: B 320 GLU cc_start: 0.7640 (tp30) cc_final: 0.7345 (tp30) REVERT: B 359 VAL cc_start: 0.7926 (p) cc_final: 0.7411 (t) REVERT: B 395 SER cc_start: 0.7804 (m) cc_final: 0.7256 (p) REVERT: B 473 LYS cc_start: 0.7992 (mttp) cc_final: 0.7112 (mtpp) REVERT: B 475 ASN cc_start: 0.7937 (t0) cc_final: 0.7522 (t0) REVERT: B 487 ILE cc_start: 0.8591 (pt) cc_final: 0.8333 (mt) REVERT: B 488 MET cc_start: 0.7134 (tpp) cc_final: 0.5795 (tpp) REVERT: B 492 LEU cc_start: 0.8637 (mt) cc_final: 0.7689 (mt) REVERT: B 499 LEU cc_start: 0.8288 (tp) cc_final: 0.8065 (tp) REVERT: B 502 LEU cc_start: 0.8067 (tp) cc_final: 0.7710 (mt) REVERT: B 503 LEU cc_start: 0.8175 (mm) cc_final: 0.7844 (mp) REVERT: B 556 TYR cc_start: 0.8284 (p90) cc_final: 0.8083 (p90) REVERT: B 583 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8697 (tttm) REVERT: B 677 ARG cc_start: 0.7483 (ttt180) cc_final: 0.7107 (ttp80) REVERT: B 682 GLU cc_start: 0.8222 (tp30) cc_final: 0.7925 (tp30) REVERT: B 687 ASP cc_start: 0.6801 (t0) cc_final: 0.6422 (t0) REVERT: B 701 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6991 (mm-30) REVERT: B 705 GLN cc_start: 0.8323 (tt0) cc_final: 0.8109 (tt0) REVERT: B 706 CYS cc_start: 0.7329 (m) cc_final: 0.7125 (m) outliers start: 55 outliers final: 35 residues processed: 335 average time/residue: 0.2457 time to fit residues: 112.0376 Evaluate side-chains 335 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 294 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0270 chunk 90 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 120 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 289 ASN A 375 HIS A 728 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10395 Z= 0.181 Angle : 0.596 8.484 14128 Z= 0.308 Chirality : 0.042 0.200 1716 Planarity : 0.004 0.054 1757 Dihedral : 5.800 83.047 1450 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.52 % Allowed : 18.88 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1319 helix: 0.13 (0.18), residues: 828 sheet: -2.24 (0.93), residues: 32 loop : -2.74 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.019 0.001 PHE B 572 TYR 0.022 0.001 TYR A 105 ARG 0.003 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 304 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7477 (mmt90) REVERT: A 37 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6418 (pm20) REVERT: A 79 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7412 (mmt90) REVERT: A 93 SER cc_start: 0.8447 (t) cc_final: 0.8090 (p) REVERT: A 122 PHE cc_start: 0.7299 (m-80) cc_final: 0.6846 (m-10) REVERT: A 123 PRO cc_start: 0.8304 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8558 (tp) cc_final: 0.7961 (tp) REVERT: A 199 ILE cc_start: 0.8226 (mt) cc_final: 0.7906 (mt) REVERT: A 213 ARG cc_start: 0.7534 (mtm180) cc_final: 0.7316 (mtm-85) REVERT: A 231 VAL cc_start: 0.8719 (t) cc_final: 0.8149 (m) REVERT: A 235 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7697 (mm-40) REVERT: A 237 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8011 (ttpp) REVERT: A 259 GLU cc_start: 0.8146 (tt0) cc_final: 0.7884 (tt0) REVERT: A 271 ASP cc_start: 0.7425 (t0) cc_final: 0.7182 (m-30) REVERT: A 279 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8723 (mm) REVERT: A 280 ILE cc_start: 0.8943 (mt) cc_final: 0.8736 (tp) REVERT: A 286 LYS cc_start: 0.9150 (tppt) cc_final: 0.8752 (mmmm) REVERT: A 355 SER cc_start: 0.7889 (m) cc_final: 0.7593 (p) REVERT: A 383 GLN cc_start: 0.7422 (mt0) cc_final: 0.7101 (mp10) REVERT: A 384 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5831 (mm-30) REVERT: A 395 SER cc_start: 0.8438 (m) cc_final: 0.8080 (p) REVERT: A 398 PHE cc_start: 0.7040 (m-80) cc_final: 0.6493 (m-80) REVERT: A 432 MET cc_start: 0.7305 (tpt) cc_final: 0.6969 (tpt) REVERT: A 447 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7892 (mttp) REVERT: A 467 ASP cc_start: 0.7349 (m-30) cc_final: 0.7124 (m-30) REVERT: A 473 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7924 (mtpt) REVERT: A 476 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8463 (mtpp) REVERT: A 478 ASP cc_start: 0.8157 (t0) cc_final: 0.7599 (t0) REVERT: A 484 PHE cc_start: 0.8189 (t80) cc_final: 0.7874 (t80) REVERT: A 488 MET cc_start: 0.7524 (tpp) cc_final: 0.7082 (tpp) REVERT: A 511 LEU cc_start: 0.8868 (mt) cc_final: 0.8650 (mt) REVERT: A 512 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8122 (ttm110) REVERT: A 530 TYR cc_start: 0.7428 (m-80) cc_final: 0.7134 (m-80) REVERT: A 546 LYS cc_start: 0.8290 (tptm) cc_final: 0.7752 (tptm) REVERT: A 556 TYR cc_start: 0.8192 (p90) cc_final: 0.7925 (p90) REVERT: A 560 ASP cc_start: 0.8058 (m-30) cc_final: 0.7854 (t0) REVERT: A 662 CYS cc_start: 0.7901 (m) cc_final: 0.7621 (m) REVERT: A 686 ILE cc_start: 0.8755 (pt) cc_final: 0.8447 (mm) REVERT: A 687 ASP cc_start: 0.6961 (t0) cc_final: 0.6513 (t0) REVERT: A 694 LEU cc_start: 0.8359 (mm) cc_final: 0.8111 (mm) REVERT: A 698 ASP cc_start: 0.7589 (t0) cc_final: 0.7378 (t0) REVERT: A 705 GLN cc_start: 0.7964 (pt0) cc_final: 0.7764 (pt0) REVERT: A 715 LYS cc_start: 0.7746 (mtpp) cc_final: 0.7172 (mmmm) REVERT: A 716 ASP cc_start: 0.7202 (t0) cc_final: 0.6857 (t0) REVERT: A 723 HIS cc_start: 0.7123 (t-170) cc_final: 0.6911 (t-90) REVERT: A 727 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.5655 (mm) REVERT: A 730 GLN cc_start: 0.8419 (mt0) cc_final: 0.7899 (mp10) REVERT: A 732 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7469 (tp-100) REVERT: B 103 MET cc_start: 0.5759 (mmt) cc_final: 0.5508 (mmp) REVERT: B 118 TYR cc_start: 0.7148 (m-10) cc_final: 0.6907 (m-80) REVERT: B 134 ARG cc_start: 0.6565 (mtt90) cc_final: 0.6322 (mtt90) REVERT: B 158 ASP cc_start: 0.5265 (m-30) cc_final: 0.3675 (m-30) REVERT: B 185 ARG cc_start: 0.6935 (mmt180) cc_final: 0.5793 (mmt180) REVERT: B 192 LEU cc_start: 0.8532 (tp) cc_final: 0.8106 (pp) REVERT: B 195 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6333 (tp) REVERT: B 199 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 207 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7449 (tm-30) REVERT: B 230 GLN cc_start: 0.7873 (tp40) cc_final: 0.7291 (tm-30) REVERT: B 231 VAL cc_start: 0.8643 (p) cc_final: 0.7832 (p) REVERT: B 235 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7237 (mm-40) REVERT: B 236 LEU cc_start: 0.8065 (tp) cc_final: 0.7662 (tp) REVERT: B 237 LYS cc_start: 0.8270 (pttt) cc_final: 0.7834 (pttt) REVERT: B 251 LEU cc_start: 0.8452 (mm) cc_final: 0.6604 (mm) REVERT: B 255 TYR cc_start: 0.8204 (m-10) cc_final: 0.7648 (m-80) REVERT: B 259 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 263 ASN cc_start: 0.7541 (t0) cc_final: 0.7020 (t0) REVERT: B 286 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7769 (tppp) REVERT: B 293 LYS cc_start: 0.8576 (pptt) cc_final: 0.8168 (mmmm) REVERT: B 320 GLU cc_start: 0.7590 (tp30) cc_final: 0.7323 (tp30) REVERT: B 324 ASN cc_start: 0.7585 (t0) cc_final: 0.7176 (t0) REVERT: B 359 VAL cc_start: 0.7900 (p) cc_final: 0.7380 (t) REVERT: B 395 SER cc_start: 0.7752 (m) cc_final: 0.7222 (p) REVERT: B 473 LYS cc_start: 0.7951 (mttp) cc_final: 0.7089 (mtpp) REVERT: B 475 ASN cc_start: 0.7939 (t0) cc_final: 0.7650 (t0) REVERT: B 484 PHE cc_start: 0.8470 (t80) cc_final: 0.8260 (t80) REVERT: B 487 ILE cc_start: 0.8542 (pt) cc_final: 0.8323 (mt) REVERT: B 488 MET cc_start: 0.7106 (tpp) cc_final: 0.5754 (tpp) REVERT: B 492 LEU cc_start: 0.8613 (mt) cc_final: 0.7662 (mt) REVERT: B 499 LEU cc_start: 0.8287 (tp) cc_final: 0.7987 (tp) REVERT: B 502 LEU cc_start: 0.7961 (tp) cc_final: 0.7474 (tp) REVERT: B 677 ARG cc_start: 0.7386 (ttt180) cc_final: 0.7053 (ttp80) REVERT: B 687 ASP cc_start: 0.6784 (t0) cc_final: 0.6382 (t0) REVERT: B 705 GLN cc_start: 0.8274 (tt0) cc_final: 0.7994 (tt0) outliers start: 62 outliers final: 38 residues processed: 341 average time/residue: 0.2473 time to fit residues: 116.3516 Evaluate side-chains 345 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 302 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 0.0170 chunk 108 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10395 Z= 0.204 Angle : 0.626 9.971 14128 Z= 0.322 Chirality : 0.042 0.231 1716 Planarity : 0.004 0.049 1757 Dihedral : 5.872 84.592 1450 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.54 % Allowed : 21.64 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1319 helix: 0.31 (0.18), residues: 815 sheet: -2.47 (0.89), residues: 34 loop : -2.62 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.017 0.001 PHE B 572 TYR 0.023 0.001 TYR A 105 ARG 0.004 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7449 (mm110) cc_final: 0.7242 (mm110) REVERT: A 36 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.7342 (mmt90) REVERT: A 37 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6455 (pm20) REVERT: A 93 SER cc_start: 0.8431 (t) cc_final: 0.8098 (p) REVERT: A 101 GLN cc_start: 0.7292 (mm110) cc_final: 0.6935 (mm-40) REVERT: A 105 TYR cc_start: 0.7379 (m-80) cc_final: 0.7143 (m-80) REVERT: A 122 PHE cc_start: 0.7269 (m-80) cc_final: 0.6836 (m-10) REVERT: A 123 PRO cc_start: 0.8305 (Cg_exo) cc_final: 0.8050 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8541 (tp) cc_final: 0.8002 (tp) REVERT: A 199 ILE cc_start: 0.8238 (mt) cc_final: 0.7893 (mt) REVERT: A 231 VAL cc_start: 0.8774 (t) cc_final: 0.8142 (p) REVERT: A 235 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7717 (mm-40) REVERT: A 237 LYS cc_start: 0.8390 (ttpp) cc_final: 0.8068 (ttpp) REVERT: A 271 ASP cc_start: 0.7444 (t0) cc_final: 0.7182 (m-30) REVERT: A 279 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 280 ILE cc_start: 0.8962 (mt) cc_final: 0.8720 (tp) REVERT: A 283 MET cc_start: 0.7796 (mpp) cc_final: 0.7538 (mpp) REVERT: A 286 LYS cc_start: 0.9119 (tppt) cc_final: 0.8774 (mmmm) REVERT: A 306 VAL cc_start: 0.8987 (p) cc_final: 0.8745 (m) REVERT: A 355 SER cc_start: 0.7898 (m) cc_final: 0.7597 (p) REVERT: A 371 TYR cc_start: 0.8118 (m-80) cc_final: 0.7783 (m-80) REVERT: A 383 GLN cc_start: 0.7330 (mt0) cc_final: 0.7085 (mt0) REVERT: A 384 GLU cc_start: 0.6553 (mm-30) cc_final: 0.5849 (mm-30) REVERT: A 395 SER cc_start: 0.8487 (m) cc_final: 0.8096 (p) REVERT: A 398 PHE cc_start: 0.7052 (m-80) cc_final: 0.6493 (m-80) REVERT: A 443 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7090 (pp20) REVERT: A 447 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7904 (mttp) REVERT: A 464 GLN cc_start: 0.8584 (mt0) cc_final: 0.8351 (mt0) REVERT: A 473 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7958 (mtpt) REVERT: A 478 ASP cc_start: 0.8135 (t0) cc_final: 0.7595 (t0) REVERT: A 484 PHE cc_start: 0.8181 (t80) cc_final: 0.7887 (t80) REVERT: A 488 MET cc_start: 0.7548 (tpp) cc_final: 0.7107 (tpp) REVERT: A 512 ARG cc_start: 0.8513 (mtm180) cc_final: 0.7344 (mtm180) REVERT: A 530 TYR cc_start: 0.7447 (m-80) cc_final: 0.7129 (m-80) REVERT: A 546 LYS cc_start: 0.8259 (tptm) cc_final: 0.7741 (tptm) REVERT: A 556 TYR cc_start: 0.8207 (p90) cc_final: 0.7987 (p90) REVERT: A 566 ILE cc_start: 0.8803 (mm) cc_final: 0.8599 (mt) REVERT: A 662 CYS cc_start: 0.7785 (m) cc_final: 0.7538 (m) REVERT: A 667 PHE cc_start: 0.7850 (p90) cc_final: 0.7440 (p90) REVERT: A 679 ILE cc_start: 0.8476 (mt) cc_final: 0.8212 (mt) REVERT: A 686 ILE cc_start: 0.8770 (pt) cc_final: 0.8450 (mm) REVERT: A 687 ASP cc_start: 0.7107 (t0) cc_final: 0.6657 (t0) REVERT: A 694 LEU cc_start: 0.8362 (mm) cc_final: 0.8101 (mm) REVERT: A 715 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7105 (mmmm) REVERT: A 716 ASP cc_start: 0.7244 (t0) cc_final: 0.6903 (t0) REVERT: A 727 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6195 (mm) REVERT: B 29 GLU cc_start: 0.7011 (mp0) cc_final: 0.6531 (mp0) REVERT: B 68 LEU cc_start: 0.8389 (mm) cc_final: 0.8085 (mt) REVERT: B 118 TYR cc_start: 0.7169 (m-10) cc_final: 0.6922 (m-80) REVERT: B 134 ARG cc_start: 0.6520 (mtt90) cc_final: 0.6261 (mtt90) REVERT: B 158 ASP cc_start: 0.5497 (m-30) cc_final: 0.3967 (m-30) REVERT: B 185 ARG cc_start: 0.7150 (mmt180) cc_final: 0.5989 (mmt180) REVERT: B 192 LEU cc_start: 0.8523 (tp) cc_final: 0.8103 (pp) REVERT: B 199 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 207 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 213 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7881 (mtm180) REVERT: B 230 GLN cc_start: 0.7897 (tp40) cc_final: 0.7287 (tm-30) REVERT: B 231 VAL cc_start: 0.8648 (p) cc_final: 0.7854 (p) REVERT: B 235 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7282 (mm-40) REVERT: B 236 LEU cc_start: 0.8069 (tp) cc_final: 0.7665 (tp) REVERT: B 237 LYS cc_start: 0.8252 (pttt) cc_final: 0.7813 (pttt) REVERT: B 251 LEU cc_start: 0.8460 (mm) cc_final: 0.6544 (mm) REVERT: B 255 TYR cc_start: 0.8206 (m-10) cc_final: 0.7661 (m-80) REVERT: B 259 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 263 ASN cc_start: 0.7546 (t0) cc_final: 0.7004 (t0) REVERT: B 286 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7802 (tppp) REVERT: B 320 GLU cc_start: 0.7622 (tp30) cc_final: 0.7333 (tp30) REVERT: B 349 MET cc_start: 0.6841 (mmm) cc_final: 0.6628 (mmp) REVERT: B 395 SER cc_start: 0.7760 (m) cc_final: 0.7233 (p) REVERT: B 473 LYS cc_start: 0.7959 (mttp) cc_final: 0.7018 (mtpp) REVERT: B 487 ILE cc_start: 0.8592 (pt) cc_final: 0.8376 (mt) REVERT: B 488 MET cc_start: 0.7117 (tpp) cc_final: 0.5771 (tpp) REVERT: B 492 LEU cc_start: 0.8645 (mt) cc_final: 0.7707 (mt) REVERT: B 499 LEU cc_start: 0.8329 (tp) cc_final: 0.8012 (tp) REVERT: B 502 LEU cc_start: 0.7970 (tp) cc_final: 0.7501 (tp) REVERT: B 526 SER cc_start: 0.8416 (m) cc_final: 0.8166 (p) REVERT: B 677 ARG cc_start: 0.7392 (ttt180) cc_final: 0.7045 (ttp80) REVERT: B 682 GLU cc_start: 0.8251 (tp30) cc_final: 0.7836 (tp30) REVERT: B 687 ASP cc_start: 0.6836 (t0) cc_final: 0.6432 (t0) REVERT: B 705 GLN cc_start: 0.8335 (tt0) cc_final: 0.8024 (tt0) REVERT: B 724 ASP cc_start: 0.7224 (m-30) cc_final: 0.6944 (m-30) outliers start: 51 outliers final: 35 residues processed: 334 average time/residue: 0.2252 time to fit residues: 103.1727 Evaluate side-chains 329 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10395 Z= 0.211 Angle : 0.626 7.398 14128 Z= 0.325 Chirality : 0.043 0.217 1716 Planarity : 0.004 0.050 1757 Dihedral : 5.411 52.016 1445 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.16 % Allowed : 21.37 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1319 helix: 0.35 (0.19), residues: 815 sheet: -2.50 (0.89), residues: 34 loop : -2.55 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.008 0.001 HIS A 723 PHE 0.025 0.001 PHE B 484 TYR 0.018 0.002 TYR A 105 ARG 0.004 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 303 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7569 (mmt90) REVERT: A 37 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: A 93 SER cc_start: 0.8437 (t) cc_final: 0.8104 (p) REVERT: A 122 PHE cc_start: 0.7253 (m-80) cc_final: 0.6782 (m-10) REVERT: A 123 PRO cc_start: 0.8220 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: A 195 LEU cc_start: 0.8569 (tp) cc_final: 0.8049 (tp) REVERT: A 199 ILE cc_start: 0.8239 (mt) cc_final: 0.7910 (mt) REVERT: A 231 VAL cc_start: 0.8773 (t) cc_final: 0.8115 (p) REVERT: A 234 SER cc_start: 0.8811 (m) cc_final: 0.8289 (t) REVERT: A 235 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7698 (mm-40) REVERT: A 237 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8084 (ttpp) REVERT: A 271 ASP cc_start: 0.7508 (t0) cc_final: 0.7229 (m-30) REVERT: A 280 ILE cc_start: 0.8966 (mt) cc_final: 0.8734 (tp) REVERT: A 283 MET cc_start: 0.7826 (mpp) cc_final: 0.7516 (mpp) REVERT: A 286 LYS cc_start: 0.9132 (tppt) cc_final: 0.8757 (mmmm) REVERT: A 303 GLU cc_start: 0.8227 (mp0) cc_final: 0.7989 (mp0) REVERT: A 304 VAL cc_start: 0.9014 (t) cc_final: 0.8678 (p) REVERT: A 306 VAL cc_start: 0.8987 (p) cc_final: 0.8775 (m) REVERT: A 355 SER cc_start: 0.7899 (m) cc_final: 0.7599 (p) REVERT: A 383 GLN cc_start: 0.7428 (mt0) cc_final: 0.7138 (mt0) REVERT: A 384 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5867 (mm-30) REVERT: A 395 SER cc_start: 0.8468 (m) cc_final: 0.8093 (p) REVERT: A 398 PHE cc_start: 0.7040 (m-80) cc_final: 0.6505 (m-80) REVERT: A 447 LYS cc_start: 0.8374 (mtpt) cc_final: 0.7886 (mttp) REVERT: A 473 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7993 (mtpt) REVERT: A 484 PHE cc_start: 0.8194 (t80) cc_final: 0.7883 (t80) REVERT: A 488 MET cc_start: 0.7555 (tpp) cc_final: 0.7143 (tpp) REVERT: A 512 ARG cc_start: 0.8510 (mtm180) cc_final: 0.8293 (mtm-85) REVERT: A 530 TYR cc_start: 0.7491 (m-80) cc_final: 0.7140 (m-80) REVERT: A 546 LYS cc_start: 0.8247 (tptm) cc_final: 0.7738 (tptm) REVERT: A 566 ILE cc_start: 0.8779 (mm) cc_final: 0.8575 (mt) REVERT: A 662 CYS cc_start: 0.7812 (m) cc_final: 0.7584 (m) REVERT: A 667 PHE cc_start: 0.7759 (p90) cc_final: 0.7421 (p90) REVERT: A 679 ILE cc_start: 0.8482 (mt) cc_final: 0.8204 (mt) REVERT: A 686 ILE cc_start: 0.8784 (pt) cc_final: 0.7818 (mm) REVERT: A 694 LEU cc_start: 0.8379 (mm) cc_final: 0.8111 (mm) REVERT: A 710 ASP cc_start: 0.7391 (p0) cc_final: 0.7071 (p0) REVERT: A 715 LYS cc_start: 0.7797 (mtpp) cc_final: 0.7104 (mmmm) REVERT: A 716 ASP cc_start: 0.7254 (t0) cc_final: 0.6927 (t0) REVERT: A 723 HIS cc_start: 0.7198 (t-90) cc_final: 0.6868 (t-90) REVERT: B 68 LEU cc_start: 0.8392 (mm) cc_final: 0.8060 (mt) REVERT: B 118 TYR cc_start: 0.7199 (m-10) cc_final: 0.6992 (m-80) REVERT: B 134 ARG cc_start: 0.6518 (mtt90) cc_final: 0.6300 (mtt90) REVERT: B 207 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 230 GLN cc_start: 0.7921 (tp40) cc_final: 0.7324 (tm-30) REVERT: B 231 VAL cc_start: 0.8646 (p) cc_final: 0.8179 (p) REVERT: B 236 LEU cc_start: 0.8015 (tp) cc_final: 0.7581 (tp) REVERT: B 237 LYS cc_start: 0.8259 (pttt) cc_final: 0.7826 (pttt) REVERT: B 251 LEU cc_start: 0.8486 (mm) cc_final: 0.6548 (mm) REVERT: B 255 TYR cc_start: 0.8224 (m-10) cc_final: 0.7688 (m-80) REVERT: B 259 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8124 (tm-30) REVERT: B 263 ASN cc_start: 0.7555 (t0) cc_final: 0.6874 (t0) REVERT: B 271 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 286 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7841 (tppp) REVERT: B 293 LYS cc_start: 0.8443 (mmmm) cc_final: 0.7986 (mmtm) REVERT: B 320 GLU cc_start: 0.7612 (tp30) cc_final: 0.7341 (tp30) REVERT: B 324 ASN cc_start: 0.7718 (t0) cc_final: 0.7413 (t0) REVERT: B 340 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7173 (pp) REVERT: B 395 SER cc_start: 0.7804 (m) cc_final: 0.7278 (p) REVERT: B 473 LYS cc_start: 0.7988 (mttp) cc_final: 0.7170 (mtpp) REVERT: B 475 ASN cc_start: 0.7962 (t0) cc_final: 0.7600 (t0) REVERT: B 487 ILE cc_start: 0.8601 (pt) cc_final: 0.8341 (mm) REVERT: B 488 MET cc_start: 0.7145 (tpp) cc_final: 0.5857 (tpp) REVERT: B 492 LEU cc_start: 0.8685 (mt) cc_final: 0.7741 (mt) REVERT: B 499 LEU cc_start: 0.8208 (tp) cc_final: 0.7923 (tp) REVERT: B 526 SER cc_start: 0.8483 (m) cc_final: 0.8248 (p) REVERT: B 677 ARG cc_start: 0.7384 (ttt180) cc_final: 0.7052 (ttp80) REVERT: B 682 GLU cc_start: 0.8243 (tp30) cc_final: 0.7828 (tp30) REVERT: B 687 ASP cc_start: 0.6869 (t0) cc_final: 0.6472 (t0) REVERT: B 705 GLN cc_start: 0.8334 (tt0) cc_final: 0.8002 (tt0) REVERT: B 724 ASP cc_start: 0.7292 (m-30) cc_final: 0.7005 (m-30) outliers start: 58 outliers final: 40 residues processed: 337 average time/residue: 0.2245 time to fit residues: 104.2464 Evaluate side-chains 340 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 297 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.244 Angle : 0.666 11.278 14128 Z= 0.345 Chirality : 0.045 0.288 1716 Planarity : 0.005 0.053 1757 Dihedral : 5.555 53.344 1445 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.81 % Allowed : 22.62 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1319 helix: 0.30 (0.18), residues: 810 sheet: -2.64 (0.87), residues: 34 loop : -2.42 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.009 0.001 HIS A 728 PHE 0.028 0.001 PHE A 210 TYR 0.032 0.002 TYR A 556 ARG 0.004 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 310 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7863 (tpp-160) cc_final: 0.7581 (mmt90) REVERT: A 37 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: A 93 SER cc_start: 0.8466 (t) cc_final: 0.8135 (p) REVERT: A 101 GLN cc_start: 0.7059 (mm110) cc_final: 0.6850 (mm-40) REVERT: A 105 TYR cc_start: 0.7415 (m-80) cc_final: 0.7024 (m-80) REVERT: A 122 PHE cc_start: 0.7200 (m-80) cc_final: 0.6731 (m-10) REVERT: A 123 PRO cc_start: 0.8239 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: A 145 SER cc_start: 0.8095 (m) cc_final: 0.7794 (p) REVERT: A 195 LEU cc_start: 0.8612 (tp) cc_final: 0.8144 (tp) REVERT: A 199 ILE cc_start: 0.8239 (mt) cc_final: 0.7893 (mt) REVERT: A 231 VAL cc_start: 0.8746 (t) cc_final: 0.8116 (p) REVERT: A 234 SER cc_start: 0.8808 (m) cc_final: 0.8257 (t) REVERT: A 235 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7680 (mm-40) REVERT: A 237 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8176 (ttpp) REVERT: A 240 LEU cc_start: 0.8412 (mm) cc_final: 0.8181 (mp) REVERT: A 271 ASP cc_start: 0.7541 (t0) cc_final: 0.7261 (m-30) REVERT: A 276 LEU cc_start: 0.8502 (mm) cc_final: 0.8204 (mm) REVERT: A 279 ILE cc_start: 0.9081 (mm) cc_final: 0.8465 (mm) REVERT: A 280 ILE cc_start: 0.8973 (mt) cc_final: 0.8744 (tp) REVERT: A 283 MET cc_start: 0.7809 (tpp) cc_final: 0.7480 (mpp) REVERT: A 286 LYS cc_start: 0.9116 (tppt) cc_final: 0.8751 (mmmm) REVERT: A 303 GLU cc_start: 0.8225 (mp0) cc_final: 0.8014 (mp0) REVERT: A 304 VAL cc_start: 0.9031 (t) cc_final: 0.8727 (p) REVERT: A 306 VAL cc_start: 0.8977 (p) cc_final: 0.8754 (m) REVERT: A 335 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 371 TYR cc_start: 0.8162 (m-80) cc_final: 0.7829 (m-80) REVERT: A 395 SER cc_start: 0.8490 (m) cc_final: 0.8121 (p) REVERT: A 447 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7920 (mttp) REVERT: A 457 ASN cc_start: 0.8201 (m110) cc_final: 0.7700 (m110) REVERT: A 473 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7942 (mtpt) REVERT: A 484 PHE cc_start: 0.8208 (t80) cc_final: 0.7914 (t80) REVERT: A 488 MET cc_start: 0.7607 (tpp) cc_final: 0.7103 (tpp) REVERT: A 511 LEU cc_start: 0.8836 (mt) cc_final: 0.8625 (mm) REVERT: A 512 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8324 (mtm-85) REVERT: A 530 TYR cc_start: 0.7587 (m-80) cc_final: 0.7260 (m-80) REVERT: A 546 LYS cc_start: 0.8256 (tptm) cc_final: 0.7698 (tptm) REVERT: A 549 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.7100 (ttm-80) REVERT: A 566 ILE cc_start: 0.8771 (mm) cc_final: 0.8566 (mt) REVERT: A 662 CYS cc_start: 0.7918 (m) cc_final: 0.7663 (m) REVERT: A 667 PHE cc_start: 0.7777 (p90) cc_final: 0.7438 (p90) REVERT: A 679 ILE cc_start: 0.8492 (mt) cc_final: 0.8248 (mt) REVERT: A 684 GLN cc_start: 0.7709 (tp40) cc_final: 0.7373 (tp40) REVERT: A 686 ILE cc_start: 0.8446 (pt) cc_final: 0.8230 (mm) REVERT: A 694 LEU cc_start: 0.8458 (mm) cc_final: 0.8224 (mm) REVERT: A 710 ASP cc_start: 0.7455 (p0) cc_final: 0.7183 (p0) REVERT: A 715 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7097 (mmmm) REVERT: A 716 ASP cc_start: 0.7293 (t0) cc_final: 0.6926 (t0) REVERT: A 723 HIS cc_start: 0.7337 (t-90) cc_final: 0.7044 (t-90) REVERT: B 32 PHE cc_start: 0.7149 (t80) cc_final: 0.6945 (t80) REVERT: B 68 LEU cc_start: 0.8427 (mm) cc_final: 0.8071 (mt) REVERT: B 207 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 230 GLN cc_start: 0.7952 (tp40) cc_final: 0.7453 (tm-30) REVERT: B 231 VAL cc_start: 0.8682 (p) cc_final: 0.8268 (p) REVERT: B 236 LEU cc_start: 0.8039 (tp) cc_final: 0.7555 (tp) REVERT: B 237 LYS cc_start: 0.8307 (pttt) cc_final: 0.7847 (pttt) REVERT: B 251 LEU cc_start: 0.8480 (mm) cc_final: 0.6582 (mm) REVERT: B 255 TYR cc_start: 0.8216 (m-10) cc_final: 0.7721 (m-80) REVERT: B 259 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 263 ASN cc_start: 0.7444 (t0) cc_final: 0.6777 (t0) REVERT: B 271 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7564 (p0) REVERT: B 293 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8109 (mmtm) REVERT: B 320 GLU cc_start: 0.7674 (tp30) cc_final: 0.7406 (tp30) REVERT: B 324 ASN cc_start: 0.7950 (t0) cc_final: 0.7665 (t0) REVERT: B 340 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6910 (pp) REVERT: B 395 SER cc_start: 0.8026 (m) cc_final: 0.7490 (p) REVERT: B 473 LYS cc_start: 0.8070 (mttp) cc_final: 0.7591 (ttpp) REVERT: B 475 ASN cc_start: 0.7995 (t0) cc_final: 0.7714 (t0) REVERT: B 487 ILE cc_start: 0.8599 (pt) cc_final: 0.8398 (mt) REVERT: B 488 MET cc_start: 0.7127 (tpp) cc_final: 0.5815 (tpp) REVERT: B 492 LEU cc_start: 0.8613 (mt) cc_final: 0.7272 (mt) REVERT: B 499 LEU cc_start: 0.8264 (tp) cc_final: 0.7965 (tp) REVERT: B 677 ARG cc_start: 0.7416 (ttt180) cc_final: 0.7113 (ttp80) REVERT: B 681 LYS cc_start: 0.8418 (ptmm) cc_final: 0.8052 (ttpp) REVERT: B 682 GLU cc_start: 0.8232 (tp30) cc_final: 0.7889 (tp30) REVERT: B 687 ASP cc_start: 0.6911 (t0) cc_final: 0.6534 (t0) REVERT: B 705 GLN cc_start: 0.8282 (tt0) cc_final: 0.7944 (tt0) REVERT: B 724 ASP cc_start: 0.7285 (m-30) cc_final: 0.7009 (m-30) outliers start: 54 outliers final: 44 residues processed: 342 average time/residue: 0.2312 time to fit residues: 108.9349 Evaluate side-chains 349 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 301 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 728 HIS A 732 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10395 Z= 0.218 Angle : 0.675 8.946 14128 Z= 0.349 Chirality : 0.045 0.397 1716 Planarity : 0.004 0.051 1757 Dihedral : 5.485 53.359 1443 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.16 % Allowed : 22.62 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1319 helix: 0.35 (0.18), residues: 814 sheet: -2.67 (0.87), residues: 34 loop : -2.36 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.008 0.001 HIS A 723 PHE 0.023 0.001 PHE B 484 TYR 0.030 0.002 TYR A 556 ARG 0.007 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 300 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7656 (mmt90) REVERT: A 37 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: A 93 SER cc_start: 0.8455 (t) cc_final: 0.8127 (p) REVERT: A 122 PHE cc_start: 0.7188 (m-80) cc_final: 0.6719 (m-10) REVERT: A 123 PRO cc_start: 0.8200 (Cg_exo) cc_final: 0.7923 (Cg_endo) REVERT: A 145 SER cc_start: 0.8175 (m) cc_final: 0.7786 (p) REVERT: A 195 LEU cc_start: 0.8607 (tp) cc_final: 0.8113 (tp) REVERT: A 199 ILE cc_start: 0.8194 (mt) cc_final: 0.7872 (mt) REVERT: A 206 LEU cc_start: 0.8082 (mt) cc_final: 0.7744 (mt) REVERT: A 231 VAL cc_start: 0.8727 (t) cc_final: 0.8050 (p) REVERT: A 235 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7709 (mm-40) REVERT: A 237 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8189 (ttpp) REVERT: A 240 LEU cc_start: 0.8405 (mm) cc_final: 0.8133 (mp) REVERT: A 271 ASP cc_start: 0.7521 (t0) cc_final: 0.7245 (m-30) REVERT: A 276 LEU cc_start: 0.8489 (mm) cc_final: 0.8202 (mm) REVERT: A 279 ILE cc_start: 0.9079 (mm) cc_final: 0.8493 (mm) REVERT: A 280 ILE cc_start: 0.8969 (mt) cc_final: 0.8738 (tp) REVERT: A 283 MET cc_start: 0.7796 (tpp) cc_final: 0.7488 (mpp) REVERT: A 286 LYS cc_start: 0.9109 (tppt) cc_final: 0.8746 (mmmm) REVERT: A 303 GLU cc_start: 0.8217 (mp0) cc_final: 0.8003 (mp0) REVERT: A 304 VAL cc_start: 0.9028 (t) cc_final: 0.8739 (p) REVERT: A 306 VAL cc_start: 0.8986 (p) cc_final: 0.8761 (m) REVERT: A 335 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 371 TYR cc_start: 0.8114 (m-80) cc_final: 0.7782 (m-80) REVERT: A 395 SER cc_start: 0.8509 (m) cc_final: 0.8149 (p) REVERT: A 447 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7907 (mttp) REVERT: A 457 ASN cc_start: 0.8205 (m110) cc_final: 0.7706 (m110) REVERT: A 473 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7924 (mtpt) REVERT: A 484 PHE cc_start: 0.8183 (t80) cc_final: 0.7865 (t80) REVERT: A 488 MET cc_start: 0.7570 (tpp) cc_final: 0.7048 (tpp) REVERT: A 511 LEU cc_start: 0.8837 (mt) cc_final: 0.8607 (mm) REVERT: A 530 TYR cc_start: 0.7589 (m-80) cc_final: 0.7359 (m-80) REVERT: A 537 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7772 (mttm) REVERT: A 546 LYS cc_start: 0.8271 (tptm) cc_final: 0.7699 (tptm) REVERT: A 566 ILE cc_start: 0.8791 (mm) cc_final: 0.8588 (mt) REVERT: A 662 CYS cc_start: 0.7877 (m) cc_final: 0.7669 (m) REVERT: A 667 PHE cc_start: 0.7757 (p90) cc_final: 0.7448 (p90) REVERT: A 684 GLN cc_start: 0.7687 (tp40) cc_final: 0.7427 (tp-100) REVERT: A 694 LEU cc_start: 0.8394 (mm) cc_final: 0.8096 (mm) REVERT: A 710 ASP cc_start: 0.7466 (p0) cc_final: 0.7131 (p0) REVERT: A 715 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7086 (mmmm) REVERT: A 716 ASP cc_start: 0.7265 (t0) cc_final: 0.6906 (t0) REVERT: A 723 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.7025 (t-90) REVERT: B 68 LEU cc_start: 0.8402 (mm) cc_final: 0.8047 (mt) REVERT: B 134 ARG cc_start: 0.6400 (mtt90) cc_final: 0.6082 (mtt90) REVERT: B 207 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 230 GLN cc_start: 0.7917 (tp40) cc_final: 0.7453 (tm-30) REVERT: B 231 VAL cc_start: 0.8617 (p) cc_final: 0.8281 (p) REVERT: B 236 LEU cc_start: 0.8039 (tp) cc_final: 0.7684 (tp) REVERT: B 237 LYS cc_start: 0.8256 (pttt) cc_final: 0.7817 (pttt) REVERT: B 251 LEU cc_start: 0.8469 (mm) cc_final: 0.6617 (mm) REVERT: B 255 TYR cc_start: 0.8205 (m-10) cc_final: 0.7691 (m-80) REVERT: B 259 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 263 ASN cc_start: 0.7527 (t0) cc_final: 0.6914 (t0) REVERT: B 271 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7554 (p0) REVERT: B 293 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8091 (mmtm) REVERT: B 320 GLU cc_start: 0.7707 (tp30) cc_final: 0.7407 (tp30) REVERT: B 324 ASN cc_start: 0.7993 (t0) cc_final: 0.7709 (t0) REVERT: B 340 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7240 (pp) REVERT: B 395 SER cc_start: 0.8014 (m) cc_final: 0.7485 (p) REVERT: B 473 LYS cc_start: 0.8125 (mttp) cc_final: 0.7562 (ttpp) REVERT: B 487 ILE cc_start: 0.8620 (pt) cc_final: 0.8412 (mt) REVERT: B 488 MET cc_start: 0.7080 (tpp) cc_final: 0.5783 (tpp) REVERT: B 492 LEU cc_start: 0.8657 (mt) cc_final: 0.7279 (mt) REVERT: B 499 LEU cc_start: 0.8249 (tp) cc_final: 0.7960 (tp) REVERT: B 677 ARG cc_start: 0.7421 (ttt180) cc_final: 0.7157 (ttp80) REVERT: B 681 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8004 (ttpp) REVERT: B 682 GLU cc_start: 0.8222 (tp30) cc_final: 0.7628 (tp30) REVERT: B 685 ARG cc_start: 0.8163 (ptp90) cc_final: 0.7691 (ptp90) REVERT: B 687 ASP cc_start: 0.6902 (t0) cc_final: 0.6531 (t0) REVERT: B 705 GLN cc_start: 0.8261 (tt0) cc_final: 0.7947 (tt0) REVERT: B 720 LEU cc_start: 0.8529 (mp) cc_final: 0.8213 (mp) REVERT: B 724 ASP cc_start: 0.7307 (m-30) cc_final: 0.7071 (m-30) outliers start: 58 outliers final: 47 residues processed: 337 average time/residue: 0.2353 time to fit residues: 109.8986 Evaluate side-chains 354 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 302 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 728 HIS Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.272 Angle : 0.715 12.082 14128 Z= 0.371 Chirality : 0.046 0.363 1716 Planarity : 0.005 0.056 1757 Dihedral : 5.614 53.885 1443 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 4.72 % Allowed : 23.15 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1319 helix: 0.26 (0.18), residues: 818 sheet: -2.78 (0.86), residues: 34 loop : -2.44 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.011 0.001 HIS A 728 PHE 0.025 0.001 PHE A 210 TYR 0.030 0.002 TYR A 556 ARG 0.006 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 300 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7731 (mm110) cc_final: 0.7483 (mm110) REVERT: A 36 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7693 (mmt90) REVERT: A 37 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: A 93 SER cc_start: 0.8559 (t) cc_final: 0.8216 (p) REVERT: A 101 GLN cc_start: 0.7198 (mm110) cc_final: 0.6867 (mm-40) REVERT: A 105 TYR cc_start: 0.7520 (m-80) cc_final: 0.7113 (m-80) REVERT: A 122 PHE cc_start: 0.7166 (m-80) cc_final: 0.6697 (m-10) REVERT: A 123 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: A 145 SER cc_start: 0.8201 (m) cc_final: 0.7833 (p) REVERT: A 195 LEU cc_start: 0.8682 (tp) cc_final: 0.8239 (tp) REVERT: A 199 ILE cc_start: 0.8223 (mt) cc_final: 0.7889 (mt) REVERT: A 231 VAL cc_start: 0.8766 (t) cc_final: 0.8115 (p) REVERT: A 234 SER cc_start: 0.8801 (m) cc_final: 0.8286 (t) REVERT: A 235 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7688 (mm-40) REVERT: A 237 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8192 (ttpp) REVERT: A 240 LEU cc_start: 0.8476 (mm) cc_final: 0.8221 (mp) REVERT: A 271 ASP cc_start: 0.7566 (t0) cc_final: 0.7330 (m-30) REVERT: A 276 LEU cc_start: 0.8464 (mm) cc_final: 0.8145 (mm) REVERT: A 279 ILE cc_start: 0.9077 (mm) cc_final: 0.8493 (mm) REVERT: A 283 MET cc_start: 0.7782 (tpp) cc_final: 0.7474 (mpp) REVERT: A 286 LYS cc_start: 0.9113 (tppt) cc_final: 0.8773 (tppt) REVERT: A 302 ILE cc_start: 0.8758 (tp) cc_final: 0.8305 (tp) REVERT: A 303 GLU cc_start: 0.8230 (mp0) cc_final: 0.7702 (mp0) REVERT: A 304 VAL cc_start: 0.9045 (t) cc_final: 0.8759 (p) REVERT: A 320 GLU cc_start: 0.6800 (tp30) cc_final: 0.6400 (tp30) REVERT: A 335 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6952 (t80) REVERT: A 371 TYR cc_start: 0.8195 (m-80) cc_final: 0.7850 (m-80) REVERT: A 385 PHE cc_start: 0.8228 (t80) cc_final: 0.8013 (t80) REVERT: A 395 SER cc_start: 0.8488 (m) cc_final: 0.8131 (p) REVERT: A 457 ASN cc_start: 0.8234 (m110) cc_final: 0.7725 (m110) REVERT: A 473 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7906 (mtpt) REVERT: A 476 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8133 (mmmm) REVERT: A 484 PHE cc_start: 0.8232 (t80) cc_final: 0.7866 (t80) REVERT: A 488 MET cc_start: 0.7668 (tpp) cc_final: 0.7105 (tpp) REVERT: A 530 TYR cc_start: 0.7583 (m-80) cc_final: 0.7363 (m-80) REVERT: A 546 LYS cc_start: 0.8264 (tptm) cc_final: 0.7681 (tptm) REVERT: A 549 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.7106 (ttm-80) REVERT: A 566 ILE cc_start: 0.8794 (mm) cc_final: 0.8586 (mt) REVERT: A 662 CYS cc_start: 0.7942 (m) cc_final: 0.7689 (m) REVERT: A 667 PHE cc_start: 0.7799 (p90) cc_final: 0.7469 (p90) REVERT: A 694 LEU cc_start: 0.8468 (mm) cc_final: 0.8228 (mm) REVERT: A 714 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7109 (mtm-85) REVERT: A 715 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7608 (mtmm) REVERT: A 716 ASP cc_start: 0.7353 (t0) cc_final: 0.6882 (t0) REVERT: B 68 LEU cc_start: 0.8425 (mm) cc_final: 0.8062 (mt) REVERT: B 134 ARG cc_start: 0.6404 (mtt90) cc_final: 0.6112 (mtt90) REVERT: B 207 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 230 GLN cc_start: 0.7975 (tp40) cc_final: 0.7485 (tm-30) REVERT: B 231 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 236 LEU cc_start: 0.8042 (tp) cc_final: 0.7663 (tp) REVERT: B 237 LYS cc_start: 0.8319 (pttt) cc_final: 0.7923 (pttt) REVERT: B 251 LEU cc_start: 0.8478 (mm) cc_final: 0.6597 (mm) REVERT: B 255 TYR cc_start: 0.8221 (m-10) cc_final: 0.7732 (m-80) REVERT: B 259 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 263 ASN cc_start: 0.7563 (t0) cc_final: 0.6796 (t0) REVERT: B 271 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7643 (p0) REVERT: B 293 LYS cc_start: 0.8575 (mmmm) cc_final: 0.8156 (mmtt) REVERT: B 320 GLU cc_start: 0.7841 (tp30) cc_final: 0.7586 (tp30) REVERT: B 324 ASN cc_start: 0.8112 (t0) cc_final: 0.7857 (t0) REVERT: B 340 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6932 (pp) REVERT: B 395 SER cc_start: 0.8037 (m) cc_final: 0.7489 (p) REVERT: B 473 LYS cc_start: 0.8104 (mttp) cc_final: 0.7639 (ttpp) REVERT: B 487 ILE cc_start: 0.8621 (pt) cc_final: 0.8407 (mt) REVERT: B 488 MET cc_start: 0.7161 (tpp) cc_final: 0.5858 (tpp) REVERT: B 492 LEU cc_start: 0.8705 (mt) cc_final: 0.7317 (mt) REVERT: B 499 LEU cc_start: 0.8263 (tp) cc_final: 0.7976 (tp) REVERT: B 677 ARG cc_start: 0.7465 (ttt180) cc_final: 0.7203 (ttp80) REVERT: B 681 LYS cc_start: 0.8436 (ptmm) cc_final: 0.8046 (ttpp) REVERT: B 682 GLU cc_start: 0.8243 (tp30) cc_final: 0.7885 (tp30) REVERT: B 687 ASP cc_start: 0.6940 (t0) cc_final: 0.6571 (t0) REVERT: B 705 GLN cc_start: 0.8296 (tt0) cc_final: 0.7961 (tt0) REVERT: B 720 LEU cc_start: 0.8458 (mp) cc_final: 0.8198 (mp) REVERT: B 724 ASP cc_start: 0.7378 (m-30) cc_final: 0.7139 (m-30) outliers start: 53 outliers final: 44 residues processed: 330 average time/residue: 0.2238 time to fit residues: 101.5520 Evaluate side-chains 339 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 290 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 732 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10395 Z= 0.228 Angle : 0.710 10.009 14128 Z= 0.365 Chirality : 0.045 0.357 1716 Planarity : 0.005 0.076 1757 Dihedral : 5.523 53.539 1441 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.18 % Rotamer: Outliers : 4.54 % Allowed : 23.86 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1319 helix: 0.36 (0.18), residues: 810 sheet: -2.81 (0.96), residues: 28 loop : -2.28 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.002 0.000 HIS A 723 PHE 0.021 0.001 PHE A 210 TYR 0.030 0.002 TYR A 556 ARG 0.007 0.001 ARG A 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 295 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7684 (mmt90) REVERT: A 37 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: A 79 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7611 (mmt90) REVERT: A 93 SER cc_start: 0.8530 (t) cc_final: 0.8179 (p) REVERT: A 122 PHE cc_start: 0.7186 (m-80) cc_final: 0.6704 (m-10) REVERT: A 123 PRO cc_start: 0.8213 (Cg_exo) cc_final: 0.7932 (Cg_endo) REVERT: A 145 SER cc_start: 0.8187 (m) cc_final: 0.7824 (p) REVERT: A 195 LEU cc_start: 0.8648 (tp) cc_final: 0.8177 (tp) REVERT: A 199 ILE cc_start: 0.8212 (mt) cc_final: 0.7894 (mt) REVERT: A 206 LEU cc_start: 0.8074 (mt) cc_final: 0.7741 (mt) REVERT: A 217 ASP cc_start: 0.7763 (m-30) cc_final: 0.7029 (m-30) REVERT: A 229 PHE cc_start: 0.8385 (m-80) cc_final: 0.8036 (t80) REVERT: A 231 VAL cc_start: 0.8741 (t) cc_final: 0.8059 (p) REVERT: A 235 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7716 (mm-40) REVERT: A 237 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8180 (ttpp) REVERT: A 240 LEU cc_start: 0.8448 (mm) cc_final: 0.8196 (mp) REVERT: A 271 ASP cc_start: 0.7524 (t0) cc_final: 0.7295 (m-30) REVERT: A 276 LEU cc_start: 0.8518 (mm) cc_final: 0.8155 (mm) REVERT: A 283 MET cc_start: 0.7752 (tpp) cc_final: 0.7501 (mpp) REVERT: A 286 LYS cc_start: 0.9112 (tppt) cc_final: 0.8660 (ttmm) REVERT: A 303 GLU cc_start: 0.8208 (mp0) cc_final: 0.7982 (mp0) REVERT: A 304 VAL cc_start: 0.9025 (t) cc_final: 0.8753 (p) REVERT: A 320 GLU cc_start: 0.6714 (tp30) cc_final: 0.6297 (tp30) REVERT: A 335 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6892 (t80) REVERT: A 371 TYR cc_start: 0.8163 (m-80) cc_final: 0.7852 (m-80) REVERT: A 395 SER cc_start: 0.8448 (m) cc_final: 0.8060 (p) REVERT: A 438 LEU cc_start: 0.8001 (tp) cc_final: 0.7752 (tp) REVERT: A 447 LYS cc_start: 0.8368 (mtpt) cc_final: 0.7829 (mttp) REVERT: A 457 ASN cc_start: 0.8199 (m110) cc_final: 0.7702 (m110) REVERT: A 459 LYS cc_start: 0.8752 (tppp) cc_final: 0.8424 (tppp) REVERT: A 473 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7961 (mtpt) REVERT: A 484 PHE cc_start: 0.8179 (t80) cc_final: 0.7872 (t80) REVERT: A 488 MET cc_start: 0.7611 (tpp) cc_final: 0.7050 (tpp) REVERT: A 530 TYR cc_start: 0.7616 (m-80) cc_final: 0.7346 (m-80) REVERT: A 537 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7841 (mttm) REVERT: A 546 LYS cc_start: 0.8280 (tptm) cc_final: 0.7679 (tptm) REVERT: A 566 ILE cc_start: 0.8797 (mm) cc_final: 0.8582 (mt) REVERT: A 662 CYS cc_start: 0.7864 (m) cc_final: 0.7661 (m) REVERT: A 667 PHE cc_start: 0.7765 (p90) cc_final: 0.7486 (p90) REVERT: A 681 LYS cc_start: 0.8115 (tptt) cc_final: 0.7100 (tptt) REVERT: A 694 LEU cc_start: 0.8414 (mm) cc_final: 0.8130 (mm) REVERT: A 715 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7087 (mmmm) REVERT: A 716 ASP cc_start: 0.7331 (t0) cc_final: 0.6882 (t0) REVERT: A 723 HIS cc_start: 0.7378 (t70) cc_final: 0.7037 (t-90) REVERT: B 68 LEU cc_start: 0.8419 (mm) cc_final: 0.8049 (mt) REVERT: B 134 ARG cc_start: 0.6400 (mtt90) cc_final: 0.6095 (mtt90) REVERT: B 207 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 230 GLN cc_start: 0.7923 (tp40) cc_final: 0.7418 (tm-30) REVERT: B 231 VAL cc_start: 0.8669 (p) cc_final: 0.8303 (p) REVERT: B 236 LEU cc_start: 0.7977 (tp) cc_final: 0.7609 (tp) REVERT: B 237 LYS cc_start: 0.8288 (pttt) cc_final: 0.7902 (pttt) REVERT: B 251 LEU cc_start: 0.8442 (mm) cc_final: 0.6560 (mm) REVERT: B 255 TYR cc_start: 0.8209 (m-10) cc_final: 0.7707 (m-80) REVERT: B 259 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 263 ASN cc_start: 0.7528 (t0) cc_final: 0.6834 (t0) REVERT: B 293 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8189 (mptt) REVERT: B 320 GLU cc_start: 0.7769 (tp30) cc_final: 0.7523 (tp30) REVERT: B 324 ASN cc_start: 0.8098 (t0) cc_final: 0.7839 (t0) REVERT: B 340 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6921 (pp) REVERT: B 395 SER cc_start: 0.8011 (m) cc_final: 0.7458 (p) REVERT: B 462 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 467 ASP cc_start: 0.7083 (m-30) cc_final: 0.6822 (t0) REVERT: B 473 LYS cc_start: 0.8075 (mttp) cc_final: 0.7609 (ttpp) REVERT: B 487 ILE cc_start: 0.8600 (pt) cc_final: 0.8390 (mt) REVERT: B 488 MET cc_start: 0.7113 (tpp) cc_final: 0.5651 (tpp) REVERT: B 492 LEU cc_start: 0.8678 (mt) cc_final: 0.7215 (mt) REVERT: B 499 LEU cc_start: 0.8207 (tp) cc_final: 0.7945 (tp) REVERT: B 677 ARG cc_start: 0.7459 (ttt180) cc_final: 0.7205 (ttp80) REVERT: B 681 LYS cc_start: 0.8424 (ptmm) cc_final: 0.8041 (ttpp) REVERT: B 682 GLU cc_start: 0.8230 (tp30) cc_final: 0.7926 (tp30) REVERT: B 687 ASP cc_start: 0.6909 (t0) cc_final: 0.6536 (t0) REVERT: B 705 GLN cc_start: 0.8301 (tt0) cc_final: 0.7952 (tt0) REVERT: B 720 LEU cc_start: 0.8512 (mp) cc_final: 0.8179 (mp) REVERT: B 724 ASP cc_start: 0.7367 (m-30) cc_final: 0.6819 (t0) outliers start: 51 outliers final: 43 residues processed: 326 average time/residue: 0.2278 time to fit residues: 101.9566 Evaluate side-chains 344 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 297 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 0.0070 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 5 optimal weight: 0.0170 chunk 75 optimal weight: 0.4980 overall best weight: 0.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.131114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111925 restraints weight = 20508.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115789 restraints weight = 11565.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118363 restraints weight = 7331.385| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 10395 Z= 0.372 Angle : 0.985 59.195 14128 Z= 0.560 Chirality : 0.045 0.432 1716 Planarity : 0.005 0.074 1757 Dihedral : 5.520 53.555 1441 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 4.45 % Allowed : 24.22 % Favored : 71.33 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1319 helix: 0.41 (0.18), residues: 804 sheet: -2.79 (0.96), residues: 28 loop : -2.24 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.018 0.001 HIS A 728 PHE 0.024 0.001 PHE A 210 TYR 0.026 0.002 TYR A 556 ARG 0.008 0.000 ARG B 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2730.76 seconds wall clock time: 49 minutes 16.52 seconds (2956.52 seconds total)