Starting phenix.real_space_refine on Mon Sep 30 09:43:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/09_2024/6acd_9589.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/09_2024/6acd_9589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/09_2024/6acd_9589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/09_2024/6acd_9589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/09_2024/6acd_9589.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/09_2024/6acd_9589.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.873 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 135 5.16 5 C 15872 2.51 5 N 4112 2.21 5 O 4726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24845 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Time building chain proxies: 14.85, per 1000 atoms: 0.60 Number of scatterers: 24845 At special positions: 0 Unit cell: (146.52, 146.52, 179.52, 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 135 16.00 O 4726 8.00 N 4112 7.00 C 15872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.02 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.04 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.02 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.01 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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: 5.50 Conformation dependent library (CDL) restraints added in 3.1 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 44 sheets defined 20.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.513A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 377' Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.555A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.580A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.884A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.906A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 4.312A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 3.753A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.898A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.706A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 887 removed outlier: 3.545A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.877A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 4.151A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 4.083A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 371 through 375 removed outlier: 3.546A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 375' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.513A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.547A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 612 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.687A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 922 removed outlier: 4.010A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.142A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1014 removed outlier: 4.000A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.627A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.781A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.939A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 141 removed outlier: 5.472A pdb=" N ALA A 237 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 306 removed outlier: 4.107A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 628 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.538A pdb=" N ASN A 526 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 539 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.385A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 642 removed outlier: 5.557A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.015A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 700 through 701 removed outlier: 3.603A pdb=" N VAL A1050 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 704 through 710 removed outlier: 3.626A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 770 removed outlier: 6.158A pdb=" N ALA B 683 " --> pdb=" O MET A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.689A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.191A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.908A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.020A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.433A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 300 through 306 removed outlier: 5.838A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AC7, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AC8, first strand: chain 'B' and resid 525 through 528 removed outlier: 4.093A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 539 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.999A pdb=" N ILE B 650 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 658 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD2, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD3, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD4, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.527A pdb=" N GLN B1095 " --> pdb=" O ILE B1086 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.507A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 252 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.157A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.168A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 139 through 141 removed outlier: 5.453A pdb=" N ALA C 237 " --> pdb=" O VAL C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 300 through 306 removed outlier: 4.471A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.629A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP C 560 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AE3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 652 removed outlier: 3.555A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 704 through 710 removed outlier: 3.668A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 1069 through 1071 removed outlier: 3.665A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1078 through 1079 844 hydrogen bonds defined for protein. 2310 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: 9.99 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7362 1.33 - 1.46: 6117 1.46 - 1.58: 11771 1.58 - 1.71: 0 1.71 - 1.83: 183 Bond restraints: 25433 Sorted by residual: bond pdb=" C PHE C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.331 1.368 -0.036 1.21e-02 6.83e+03 8.96e+00 bond pdb=" CA THR C 517 " pdb=" C THR C 517 " ideal model delta sigma weight residual 1.525 1.466 0.059 2.10e-02 2.27e+03 7.79e+00 bond pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.29e+00 bond pdb=" C LYS C 142 " pdb=" N PRO C 143 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.94e+00 bond pdb=" C LYS B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.332 1.349 -0.017 8.90e-03 1.26e+04 3.55e+00 ... (remaining 25428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 34303 4.05 - 8.10: 283 8.10 - 12.14: 23 12.14 - 16.19: 3 16.19 - 20.24: 1 Bond angle restraints: 34613 Sorted by residual: angle pdb=" N THR C 517 " pdb=" CA THR C 517 " pdb=" C THR C 517 " ideal model delta sigma weight residual 111.00 131.24 -20.24 2.80e+00 1.28e-01 5.22e+01 angle pdb=" N ILE C 891 " pdb=" CA ILE C 891 " pdb=" C ILE C 891 " ideal model delta sigma weight residual 113.71 107.02 6.69 9.50e-01 1.11e+00 4.96e+01 angle pdb=" C THR C 517 " pdb=" N ASP C 518 " pdb=" CA ASP C 518 " ideal model delta sigma weight residual 121.54 108.48 13.06 1.91e+00 2.74e-01 4.67e+01 angle pdb=" N GLY A 634 " pdb=" CA GLY A 634 " pdb=" C GLY A 634 " ideal model delta sigma weight residual 111.63 117.99 -6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C LYS B 968 " pdb=" N VAL B 969 " pdb=" CA VAL B 969 " ideal model delta sigma weight residual 120.62 129.43 -8.81 1.64e+00 3.72e-01 2.89e+01 ... (remaining 34608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14522 17.87 - 35.74: 469 35.74 - 53.60: 96 53.60 - 71.47: 24 71.47 - 89.34: 8 Dihedral angle restraints: 15119 sinusoidal: 5833 harmonic: 9286 Sorted by residual: dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -109.21 -70.79 0 5.00e+00 4.00e-02 2.00e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -113.59 -66.41 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -175.34 89.34 1 1.00e+01 1.00e-02 9.49e+01 ... (remaining 15116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3818 0.140 - 0.280: 99 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 1 Chirality restraints: 3918 Sorted by residual: chirality pdb=" CA THR C 517 " pdb=" N THR C 517 " pdb=" C THR C 517 " pdb=" CB THR C 517 " both_signs ideal model delta sigma weight residual False 2.53 1.83 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU A 745 " pdb=" CB LEU A 745 " pdb=" CD1 LEU A 745 " pdb=" CD2 LEU A 745 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB THR A 71 " pdb=" CA THR A 71 " pdb=" OG1 THR A 71 " pdb=" CG2 THR A 71 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3915 not shown) Planarity restraints: 4485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 678 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR A 678 " 0.058 2.00e-02 2.50e+03 pdb=" O THR A 678 " -0.022 2.00e-02 2.50e+03 pdb=" N MET A 679 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 678 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C THR B 678 " -0.057 2.00e-02 2.50e+03 pdb=" O THR B 678 " 0.021 2.00e-02 2.50e+03 pdb=" N MET B 679 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 517 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR C 517 " 0.056 2.00e-02 2.50e+03 pdb=" O THR C 517 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP C 518 " -0.018 2.00e-02 2.50e+03 ... (remaining 4482 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 5 2.28 - 2.94: 11203 2.94 - 3.59: 34304 3.59 - 4.25: 56511 4.25 - 4.90: 92829 Nonbonded interactions: 194852 Sorted by model distance: nonbonded pdb=" O VAL C 314 " pdb=" CG2 THR C 517 " model vdw 1.629 3.460 nonbonded pdb=" OG SER A 95 " pdb=" O SER A 173 " model vdw 2.242 3.040 nonbonded pdb=" O GLN C 939 " pdb=" OG1 THR C 943 " model vdw 2.246 3.040 nonbonded pdb=" OG SER C 95 " pdb=" O SER C 173 " model vdw 2.262 3.040 nonbonded pdb=" OG SER B 95 " pdb=" O SER B 173 " model vdw 2.281 3.040 ... (remaining 194847 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 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.360 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 63.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.007 0.080 25433 Z= 0.432 Angle : 1.044 20.239 34613 Z= 0.585 Chirality : 0.060 0.700 3918 Planarity : 0.008 0.073 4485 Dihedral : 9.719 83.092 9030 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.34 % Favored : 85.12 % Rotamer: Outliers : 0.25 % Allowed : 2.14 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.47 (0.12), residues: 3159 helix: -1.53 (0.17), residues: 635 sheet: -2.07 (0.20), residues: 567 loop : -4.01 (0.11), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 868 HIS 0.013 0.002 HIS C1046 PHE 0.034 0.004 PHE B 837 TYR 0.028 0.003 TYR B 300 ARG 0.011 0.001 ARG C 797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 571 time to evaluate : 2.790 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: symmetry clash REVERT: A 164 ILE cc_start: 0.9361 (mt) cc_final: 0.9129 (tp) REVERT: A 215 THR cc_start: 0.8560 (m) cc_final: 0.8288 (p) REVERT: A 245 TRP cc_start: 0.4032 (p-90) cc_final: 0.2769 (p-90) REVERT: A 360 PHE cc_start: 0.8056 (t80) cc_final: 0.7754 (m-10) REVERT: A 480 ASP cc_start: 0.8697 (m-30) cc_final: 0.8308 (t70) REVERT: A 491 TYR cc_start: 0.8606 (m-10) cc_final: 0.8281 (m-80) REVERT: A 502 GLU cc_start: 0.6107 (tt0) cc_final: 0.5901 (tt0) REVERT: A 519 LEU cc_start: 0.8854 (mp) cc_final: 0.8339 (tt) REVERT: A 687 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 752 ILE cc_start: 0.9011 (mt) cc_final: 0.8456 (mm) REVERT: B 96 ASN cc_start: 0.8145 (m-40) cc_final: 0.7516 (m-40) REVERT: B 300 TYR cc_start: 0.8878 (m-10) cc_final: 0.8536 (m-10) REVERT: B 571 LEU cc_start: 0.8937 (mt) cc_final: 0.8715 (tp) REVERT: B 738 TYR cc_start: 0.8281 (m-10) cc_final: 0.6685 (m-10) REVERT: B 1091 PHE cc_start: 0.8548 (t80) cc_final: 0.8347 (t80) REVERT: B 1101 ASN cc_start: 0.7982 (m-40) cc_final: 0.7663 (t0) REVERT: C 220 PHE cc_start: 0.7994 (m-10) cc_final: 0.7752 (m-80) REVERT: C 274 ASP cc_start: 0.7856 (t0) cc_final: 0.7560 (t0) REVERT: C 287 LYS cc_start: 0.9276 (mttt) cc_final: 0.9020 (mtpt) REVERT: C 289 SER cc_start: 0.8033 (m) cc_final: 0.7671 (p) REVERT: C 300 TYR cc_start: 0.8989 (m-10) cc_final: 0.8729 (m-10) REVERT: C 417 MET cc_start: -0.2484 (tpt) cc_final: -0.2733 (mmp) REVERT: C 528 ASN cc_start: 0.8590 (t0) cc_final: 0.8094 (t0) REVERT: C 738 TYR cc_start: 0.9017 (m-10) cc_final: 0.8563 (m-80) outliers start: 7 outliers final: 1 residues processed: 577 average time/residue: 0.3930 time to fit residues: 341.9294 Evaluate side-chains 297 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 181 HIS A 505 ASN A 699 ASN A 769 GLN A 931 GLN A 993 GLN A1005 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 56 GLN B 129 ASN B 181 HIS ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 699 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN B 883 GLN B1088 GLN B1101 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 181 HIS C 744 GLN C 759 ASN C 766 GLN C 896 ASN C 947 GLN C 984 GLN C 987 GLN C 993 GLN C1005 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 25433 Z= 0.217 Angle : 0.731 10.423 34613 Z= 0.388 Chirality : 0.048 0.295 3918 Planarity : 0.006 0.059 4485 Dihedral : 6.933 63.677 3425 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.90 % Favored : 87.78 % Rotamer: Outliers : 1.81 % Allowed : 9.25 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.56 (0.13), residues: 3159 helix: 0.02 (0.20), residues: 622 sheet: -1.76 (0.22), residues: 556 loop : -3.60 (0.11), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 423 HIS 0.010 0.001 HIS C1030 PHE 0.027 0.002 PHE B1077 TYR 0.020 0.001 TYR C 723 ARG 0.007 0.001 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 367 time to evaluate : 2.722 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.9368 (mt) cc_final: 0.9016 (tp) REVERT: A 245 TRP cc_start: 0.4282 (p-90) cc_final: 0.3008 (p-90) REVERT: A 253 PHE cc_start: 0.8725 (m-10) cc_final: 0.8390 (m-10) REVERT: A 361 PHE cc_start: 0.7307 (m-10) cc_final: 0.7066 (m-10) REVERT: A 439 LYS cc_start: 0.7434 (pttt) cc_final: 0.7164 (ptpt) REVERT: A 491 TYR cc_start: 0.8593 (m-10) cc_final: 0.8180 (m-80) REVERT: A 519 LEU cc_start: 0.8790 (mp) cc_final: 0.8176 (tt) REVERT: A 687 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8020 (tp) REVERT: A 840 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8759 (pp) REVERT: B 107 MET cc_start: 0.2810 (mmp) cc_final: 0.0144 (mtt) REVERT: B 151 MET cc_start: 0.3029 (ptm) cc_final: 0.2460 (ptt) REVERT: B 379 PHE cc_start: 0.7330 (m-10) cc_final: 0.7128 (m-80) REVERT: B 560 ASP cc_start: 0.7778 (t0) cc_final: 0.7453 (t0) REVERT: B 918 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8356 (tp30) REVERT: B 1101 ASN cc_start: 0.8096 (m110) cc_final: 0.7652 (t0) REVERT: C 184 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6735 (pt0) REVERT: C 274 ASP cc_start: 0.7475 (t0) cc_final: 0.7199 (t0) REVERT: C 287 LYS cc_start: 0.9425 (mttt) cc_final: 0.9085 (mtpt) REVERT: C 302 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8569 (t) REVERT: C 528 ASN cc_start: 0.8507 (t0) cc_final: 0.7821 (t0) REVERT: C 723 TYR cc_start: 0.8715 (t80) cc_final: 0.8252 (t80) REVERT: C 884 MET cc_start: 0.8048 (mtt) cc_final: 0.7824 (mtt) REVERT: C 947 GLN cc_start: 0.8510 (mm110) cc_final: 0.8134 (mp10) REVERT: C 1089 ARG cc_start: 0.7765 (ttt180) cc_final: 0.7374 (mmm160) outliers start: 50 outliers final: 19 residues processed: 399 average time/residue: 0.3533 time to fit residues: 224.6043 Evaluate side-chains 285 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 927 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 239 optimal weight: 0.0980 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 288 optimal weight: 6.9990 chunk 311 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 285 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 231 optimal weight: 0.0270 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 505 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 937 ASN B 984 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 25433 Z= 0.186 Angle : 0.700 10.306 34613 Z= 0.367 Chirality : 0.048 0.224 3918 Planarity : 0.005 0.059 4485 Dihedral : 6.410 63.398 3424 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.33 % Favored : 88.38 % Rotamer: Outliers : 2.39 % Allowed : 10.26 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.13 (0.14), residues: 3159 helix: 0.65 (0.21), residues: 610 sheet: -1.43 (0.22), residues: 555 loop : -3.41 (0.12), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.007 0.001 HIS C1030 PHE 0.020 0.001 PHE B 837 TYR 0.018 0.001 TYR C 723 ARG 0.011 0.001 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 327 time to evaluate : 2.790 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: symmetry clash REVERT: A 37 MET cc_start: 0.7962 (mmp) cc_final: 0.7698 (mmp) REVERT: A 54 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9045 (tt) REVERT: A 164 ILE cc_start: 0.9419 (mt) cc_final: 0.9064 (tp) REVERT: A 245 TRP cc_start: 0.4176 (p-90) cc_final: 0.2948 (p-90) REVERT: A 253 PHE cc_start: 0.8573 (m-10) cc_final: 0.8086 (m-10) REVERT: A 299 ILE cc_start: 0.9070 (tp) cc_final: 0.8546 (tt) REVERT: A 393 ASP cc_start: 0.8640 (m-30) cc_final: 0.8174 (m-30) REVERT: A 414 ASP cc_start: 0.7646 (p0) cc_final: 0.7415 (p0) REVERT: A 423 TRP cc_start: 0.8354 (p-90) cc_final: 0.7616 (p90) REVERT: A 491 TYR cc_start: 0.8594 (m-10) cc_final: 0.8186 (m-80) REVERT: A 500 SER cc_start: 0.9312 (t) cc_final: 0.8673 (p) REVERT: A 502 GLU cc_start: 0.5802 (tt0) cc_final: 0.5273 (mt-10) REVERT: A 687 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8015 (tp) REVERT: A 721 ASN cc_start: 0.8500 (t0) cc_final: 0.8210 (t0) REVERT: A 741 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: B 44 ASP cc_start: 0.8716 (t70) cc_final: 0.8435 (t70) REVERT: B 87 ILE cc_start: 0.8834 (pt) cc_final: 0.8500 (mt) REVERT: B 151 MET cc_start: 0.2131 (ptm) cc_final: 0.1811 (ptt) REVERT: B 186 VAL cc_start: 0.9468 (t) cc_final: 0.9239 (m) REVERT: B 327 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8084 (mp0) REVERT: B 677 TYR cc_start: 0.7667 (p90) cc_final: 0.7030 (p90) REVERT: B 741 PHE cc_start: 0.7309 (t80) cc_final: 0.7008 (t80) REVERT: B 755 GLU cc_start: 0.8822 (tt0) cc_final: 0.8479 (tp30) REVERT: B 918 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8358 (tp30) REVERT: C 184 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6846 (pt0) REVERT: C 231 PHE cc_start: 0.8789 (p90) cc_final: 0.8121 (p90) REVERT: C 274 ASP cc_start: 0.7357 (t0) cc_final: 0.7114 (t0) REVERT: C 287 LYS cc_start: 0.9289 (mttt) cc_final: 0.8846 (mtpt) REVERT: C 528 ASN cc_start: 0.7994 (t0) cc_final: 0.7455 (t0) REVERT: C 723 TYR cc_start: 0.8630 (t80) cc_final: 0.8224 (t80) REVERT: C 868 TRP cc_start: 0.5821 (t60) cc_final: 0.5241 (t60) REVERT: C 877 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5746 (tm-30) REVERT: C 930 LEU cc_start: 0.8948 (mt) cc_final: 0.8704 (mp) REVERT: C 947 GLN cc_start: 0.8631 (mm110) cc_final: 0.8289 (mp10) REVERT: C 1085 PHE cc_start: 0.7470 (m-80) cc_final: 0.7211 (m-80) REVERT: C 1089 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7340 (mmm160) outliers start: 66 outliers final: 33 residues processed: 378 average time/residue: 0.3505 time to fit residues: 211.2331 Evaluate side-chains 293 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 193 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 274 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 744 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 GLN B 746 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25433 Z= 0.263 Angle : 0.705 10.168 34613 Z= 0.369 Chirality : 0.047 0.270 3918 Planarity : 0.005 0.059 4485 Dihedral : 6.319 63.984 3424 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.28 % Favored : 87.43 % Rotamer: Outliers : 3.08 % Allowed : 11.42 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.96 (0.14), residues: 3159 helix: 0.85 (0.21), residues: 612 sheet: -1.39 (0.22), residues: 575 loop : -3.31 (0.12), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 423 HIS 0.012 0.001 HIS C1030 PHE 0.034 0.002 PHE B 837 TYR 0.019 0.001 TYR C 855 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 253 time to evaluate : 2.599 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: A 54 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9187 (tt) REVERT: A 80 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8384 (p) REVERT: A 107 MET cc_start: 0.7886 (mtt) cc_final: 0.7656 (mtt) REVERT: A 245 TRP cc_start: 0.4479 (p-90) cc_final: 0.3302 (p-90) REVERT: A 253 PHE cc_start: 0.8686 (m-10) cc_final: 0.8465 (m-10) REVERT: A 393 ASP cc_start: 0.8759 (m-30) cc_final: 0.8474 (m-30) REVERT: A 414 ASP cc_start: 0.7632 (p0) cc_final: 0.7384 (p0) REVERT: A 491 TYR cc_start: 0.8639 (m-10) cc_final: 0.8242 (m-80) REVERT: A 500 SER cc_start: 0.9280 (t) cc_final: 0.8623 (p) REVERT: A 502 GLU cc_start: 0.5872 (tt0) cc_final: 0.5402 (mt-10) REVERT: A 687 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 882 MET cc_start: 0.8292 (mtp) cc_final: 0.7985 (mtp) REVERT: B 107 MET cc_start: 0.2999 (mmp) cc_final: 0.0195 (mtt) REVERT: B 285 GLU cc_start: 0.8608 (tp30) cc_final: 0.8245 (tp30) REVERT: B 679 MET cc_start: 0.7926 (tpp) cc_final: 0.7401 (tpp) REVERT: B 1013 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: C 184 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6891 (pt0) REVERT: C 231 PHE cc_start: 0.8778 (p90) cc_final: 0.8159 (p90) REVERT: C 274 ASP cc_start: 0.7694 (t0) cc_final: 0.7465 (t0) REVERT: C 287 LYS cc_start: 0.9316 (mttt) cc_final: 0.8953 (mtpt) REVERT: C 528 ASN cc_start: 0.8198 (t0) cc_final: 0.7700 (t0) REVERT: C 718 VAL cc_start: 0.9436 (t) cc_final: 0.9206 (p) REVERT: C 883 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: C 1089 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7451 (mmm160) outliers start: 85 outliers final: 52 residues processed: 316 average time/residue: 0.3377 time to fit residues: 173.7183 Evaluate side-chains 285 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 227 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 211 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN A 947 GLN ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25433 Z= 0.288 Angle : 0.702 10.458 34613 Z= 0.369 Chirality : 0.047 0.284 3918 Planarity : 0.005 0.058 4485 Dihedral : 6.256 62.125 3424 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.79 % Favored : 86.93 % Rotamer: Outliers : 2.97 % Allowed : 11.68 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.88 (0.14), residues: 3159 helix: 0.87 (0.21), residues: 630 sheet: -1.27 (0.23), residues: 544 loop : -3.28 (0.12), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 423 HIS 0.010 0.001 HIS C1030 PHE 0.033 0.002 PHE B 837 TYR 0.018 0.001 TYR B 689 ARG 0.005 0.001 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 238 time to evaluate : 2.535 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: A 54 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9183 (tt) REVERT: A 80 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 245 TRP cc_start: 0.4580 (p-90) cc_final: 0.3522 (p-90) REVERT: A 393 ASP cc_start: 0.8786 (m-30) cc_final: 0.8537 (m-30) REVERT: A 414 ASP cc_start: 0.7661 (p0) cc_final: 0.7397 (p0) REVERT: A 491 TYR cc_start: 0.8624 (m-10) cc_final: 0.8149 (m-80) REVERT: A 500 SER cc_start: 0.9268 (t) cc_final: 0.8681 (p) REVERT: A 502 GLU cc_start: 0.5853 (tt0) cc_final: 0.5419 (mt-10) REVERT: A 882 MET cc_start: 0.8352 (mtp) cc_final: 0.8006 (mtp) REVERT: A 946 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8897 (tptp) REVERT: A 966 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7394 (pp) REVERT: B 87 ILE cc_start: 0.8623 (pt) cc_final: 0.8246 (mt) REVERT: B 107 MET cc_start: 0.3280 (mmp) cc_final: 0.0383 (mtt) REVERT: B 151 MET cc_start: 0.4720 (ptt) cc_final: 0.4505 (ptt) REVERT: B 679 MET cc_start: 0.8285 (tpp) cc_final: 0.7588 (tpp) REVERT: B 721 ASN cc_start: 0.8798 (m-40) cc_final: 0.8239 (t0) REVERT: B 746 ASN cc_start: 0.8199 (m-40) cc_final: 0.7479 (m-40) REVERT: B 1013 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: C 184 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6828 (pt0) REVERT: C 231 PHE cc_start: 0.8910 (p90) cc_final: 0.8196 (p90) REVERT: C 274 ASP cc_start: 0.7863 (t0) cc_final: 0.7624 (t0) REVERT: C 287 LYS cc_start: 0.9307 (mttt) cc_final: 0.8864 (mtpt) REVERT: C 528 ASN cc_start: 0.8050 (t0) cc_final: 0.7547 (t0) REVERT: C 1089 ARG cc_start: 0.7787 (ttt90) cc_final: 0.7258 (mmm160) outliers start: 82 outliers final: 54 residues processed: 304 average time/residue: 0.3264 time to fit residues: 163.1319 Evaluate side-chains 276 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 967 ASP Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 306 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 599 GLN B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 25433 Z= 0.207 Angle : 0.678 13.015 34613 Z= 0.355 Chirality : 0.046 0.229 3918 Planarity : 0.004 0.058 4485 Dihedral : 6.075 60.571 3422 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.78 % Favored : 87.97 % Rotamer: Outliers : 2.76 % Allowed : 12.29 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.66 (0.14), residues: 3159 helix: 1.40 (0.22), residues: 580 sheet: -1.32 (0.22), residues: 588 loop : -3.11 (0.12), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 868 HIS 0.009 0.001 HIS C1030 PHE 0.033 0.001 PHE B 837 TYR 0.017 0.001 TYR B 689 ARG 0.008 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 261 time to evaluate : 2.867 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: A 54 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9203 (tt) REVERT: A 80 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 367 TYR cc_start: 0.8162 (m-10) cc_final: 0.7904 (m-10) REVERT: A 393 ASP cc_start: 0.8746 (m-30) cc_final: 0.8514 (m-30) REVERT: A 491 TYR cc_start: 0.8627 (m-10) cc_final: 0.8180 (m-80) REVERT: A 500 SER cc_start: 0.9269 (t) cc_final: 0.8680 (p) REVERT: A 502 GLU cc_start: 0.5720 (tt0) cc_final: 0.5341 (mt-10) REVERT: A 510 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8284 (m) REVERT: A 838 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 882 MET cc_start: 0.8251 (mtp) cc_final: 0.7932 (mtp) REVERT: B 87 ILE cc_start: 0.8833 (pt) cc_final: 0.8500 (mt) REVERT: B 107 MET cc_start: 0.3225 (mmp) cc_final: 0.0375 (mtt) REVERT: B 285 GLU cc_start: 0.8676 (tp30) cc_final: 0.8365 (tp30) REVERT: B 679 MET cc_start: 0.8346 (tpp) cc_final: 0.7788 (tpp) REVERT: B 1013 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: C 184 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6872 (pt0) REVERT: C 231 PHE cc_start: 0.8928 (p90) cc_final: 0.8387 (p90) REVERT: C 287 LYS cc_start: 0.9381 (mttt) cc_final: 0.8987 (mtpt) REVERT: C 528 ASN cc_start: 0.7969 (t0) cc_final: 0.7457 (t0) REVERT: C 868 TRP cc_start: 0.5498 (t60) cc_final: 0.5020 (t60) REVERT: C 930 LEU cc_start: 0.9049 (mt) cc_final: 0.8841 (mp) REVERT: C 1089 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7274 (mmm160) outliers start: 76 outliers final: 48 residues processed: 319 average time/residue: 0.3201 time to fit residues: 168.7588 Evaluate side-chains 274 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 258 optimal weight: 30.0000 chunk 171 optimal weight: 8.9990 chunk 305 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25433 Z= 0.215 Angle : 0.680 14.998 34613 Z= 0.355 Chirality : 0.046 0.208 3918 Planarity : 0.004 0.057 4485 Dihedral : 6.000 60.019 3422 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.44 % Favored : 87.34 % Rotamer: Outliers : 2.97 % Allowed : 13.05 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.64 (0.15), residues: 3159 helix: 1.30 (0.22), residues: 587 sheet: -1.27 (0.22), residues: 588 loop : -3.09 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 423 HIS 0.008 0.001 HIS C1030 PHE 0.041 0.001 PHE B 837 TYR 0.021 0.001 TYR A 367 ARG 0.007 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 232 time to evaluate : 2.663 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: A 54 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9208 (tt) REVERT: A 245 TRP cc_start: 0.4446 (p-90) cc_final: 0.4110 (p-90) REVERT: A 367 TYR cc_start: 0.8390 (m-10) cc_final: 0.8164 (m-10) REVERT: A 393 ASP cc_start: 0.8764 (m-30) cc_final: 0.8553 (m-30) REVERT: A 491 TYR cc_start: 0.8627 (m-10) cc_final: 0.8173 (m-80) REVERT: A 502 GLU cc_start: 0.5813 (tt0) cc_final: 0.5482 (mt-10) REVERT: A 510 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8225 (m) REVERT: A 721 ASN cc_start: 0.8955 (m-40) cc_final: 0.8648 (t0) REVERT: A 838 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7585 (p0) REVERT: A 882 MET cc_start: 0.8268 (mtp) cc_final: 0.7941 (mtp) REVERT: A 984 GLN cc_start: 0.8589 (mm110) cc_final: 0.8061 (tp40) REVERT: A 1011 MET cc_start: 0.8086 (tpp) cc_final: 0.7578 (tpp) REVERT: B 107 MET cc_start: 0.3259 (mmp) cc_final: 0.0391 (mtt) REVERT: B 285 GLU cc_start: 0.8672 (tp30) cc_final: 0.8368 (tp30) REVERT: B 679 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7892 (tpp) REVERT: B 1013 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: C 184 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: C 231 PHE cc_start: 0.8972 (p90) cc_final: 0.8451 (p90) REVERT: C 274 ASP cc_start: 0.7797 (t0) cc_final: 0.7541 (t0) REVERT: C 287 LYS cc_start: 0.9266 (mttt) cc_final: 0.8851 (mtpt) REVERT: C 528 ASN cc_start: 0.8137 (t0) cc_final: 0.7709 (t0) REVERT: C 1089 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7274 (mmm160) outliers start: 82 outliers final: 59 residues processed: 295 average time/residue: 0.3181 time to fit residues: 156.0749 Evaluate side-chains 279 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 214 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25433 Z= 0.221 Angle : 0.680 12.723 34613 Z= 0.354 Chirality : 0.047 0.309 3918 Planarity : 0.004 0.057 4485 Dihedral : 5.929 59.578 3422 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.12 % Favored : 87.65 % Rotamer: Outliers : 2.97 % Allowed : 13.45 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.57 (0.15), residues: 3159 helix: 1.31 (0.22), residues: 586 sheet: -1.25 (0.22), residues: 590 loop : -3.02 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 101 HIS 0.008 0.001 HIS C1030 PHE 0.035 0.001 PHE B 837 TYR 0.021 0.001 TYR C 723 ARG 0.007 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 228 time to evaluate : 3.133 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: A 54 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9204 (tt) REVERT: A 393 ASP cc_start: 0.8779 (m-30) cc_final: 0.8507 (m-30) REVERT: A 491 TYR cc_start: 0.8624 (m-10) cc_final: 0.8164 (m-80) REVERT: A 510 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8182 (m) REVERT: A 721 ASN cc_start: 0.8865 (m-40) cc_final: 0.8545 (t0) REVERT: A 762 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 838 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7586 (p0) REVERT: A 882 MET cc_start: 0.8306 (mtp) cc_final: 0.7985 (mtp) REVERT: A 918 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 107 MET cc_start: 0.3351 (mmp) cc_final: 0.0435 (mtt) REVERT: B 285 GLU cc_start: 0.8673 (tp30) cc_final: 0.8364 (tp30) REVERT: B 679 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: B 1013 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: C 184 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6936 (pt0) REVERT: C 231 PHE cc_start: 0.8981 (p90) cc_final: 0.8441 (p90) REVERT: C 287 LYS cc_start: 0.9213 (mttt) cc_final: 0.8891 (mtpt) REVERT: C 528 ASN cc_start: 0.8159 (t0) cc_final: 0.7760 (t0) REVERT: C 558 PHE cc_start: 0.7411 (m-10) cc_final: 0.6883 (m-10) REVERT: C 1032 MET cc_start: 0.7823 (mmm) cc_final: 0.7568 (mmm) REVERT: C 1089 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7255 (mmm160) outliers start: 82 outliers final: 62 residues processed: 292 average time/residue: 0.3164 time to fit residues: 154.6154 Evaluate side-chains 282 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 214 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 4.9990 chunk 292 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 284 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25433 Z= 0.237 Angle : 0.688 12.424 34613 Z= 0.358 Chirality : 0.047 0.299 3918 Planarity : 0.004 0.056 4485 Dihedral : 5.898 59.256 3422 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.38 % Favored : 87.40 % Rotamer: Outliers : 2.76 % Allowed : 13.96 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.56 (0.15), residues: 3159 helix: 1.21 (0.22), residues: 600 sheet: -1.17 (0.22), residues: 576 loop : -3.02 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 245 HIS 0.008 0.001 HIS C1030 PHE 0.033 0.001 PHE B 837 TYR 0.017 0.001 TYR C 723 ARG 0.006 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 218 time to evaluate : 2.462 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 54 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9210 (tt) REVERT: A 393 ASP cc_start: 0.8799 (m-30) cc_final: 0.8530 (m-30) REVERT: A 491 TYR cc_start: 0.8658 (m-10) cc_final: 0.8204 (m-80) REVERT: A 510 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8197 (m) REVERT: A 721 ASN cc_start: 0.8896 (m-40) cc_final: 0.8561 (t0) REVERT: A 838 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 918 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7994 (mt-10) REVERT: B 80 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7243 (p) REVERT: B 285 GLU cc_start: 0.8696 (tp30) cc_final: 0.8370 (tp30) REVERT: B 679 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8009 (tpp) REVERT: B 721 ASN cc_start: 0.8347 (m-40) cc_final: 0.6913 (t0) REVERT: B 868 TRP cc_start: 0.5799 (t60) cc_final: 0.5585 (p-90) REVERT: B 1013 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: C 181 HIS cc_start: 0.7691 (m90) cc_final: 0.7463 (m90) REVERT: C 184 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: C 231 PHE cc_start: 0.8984 (p90) cc_final: 0.8453 (p90) REVERT: C 274 ASP cc_start: 0.7771 (t0) cc_final: 0.7522 (t0) REVERT: C 287 LYS cc_start: 0.9179 (mttt) cc_final: 0.8922 (mttm) REVERT: C 528 ASN cc_start: 0.8157 (t0) cc_final: 0.7760 (t0) REVERT: C 558 PHE cc_start: 0.7443 (m-10) cc_final: 0.6926 (m-10) REVERT: C 972 GLU cc_start: 0.8599 (mp0) cc_final: 0.8094 (mp0) REVERT: C 1032 MET cc_start: 0.7857 (mmm) cc_final: 0.7629 (mmm) REVERT: C 1089 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7418 (mmm160) outliers start: 76 outliers final: 60 residues processed: 279 average time/residue: 0.3132 time to fit residues: 145.9451 Evaluate side-chains 276 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 209 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 946 LYS Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 4.9990 chunk 301 optimal weight: 0.0670 chunk 183 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 315 optimal weight: 0.0170 chunk 290 optimal weight: 3.9990 chunk 251 optimal weight: 30.0000 chunk 26 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25433 Z= 0.179 Angle : 0.673 12.559 34613 Z= 0.350 Chirality : 0.047 0.312 3918 Planarity : 0.004 0.057 4485 Dihedral : 5.744 58.658 3422 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.30 % Favored : 88.48 % Rotamer: Outliers : 2.25 % Allowed : 14.32 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.44 (0.15), residues: 3159 helix: 1.34 (0.22), residues: 595 sheet: -0.97 (0.22), residues: 600 loop : -3.00 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 245 HIS 0.007 0.001 HIS C1030 PHE 0.031 0.001 PHE B 837 TYR 0.013 0.001 TYR C 723 ARG 0.006 0.000 ARG B 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 258 time to evaluate : 2.745 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 54 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9199 (tt) REVERT: A 367 TYR cc_start: 0.8083 (m-10) cc_final: 0.7869 (m-10) REVERT: A 393 ASP cc_start: 0.8771 (m-30) cc_final: 0.8516 (m-30) REVERT: A 410 TYR cc_start: 0.5707 (t80) cc_final: 0.5431 (t80) REVERT: A 491 TYR cc_start: 0.8692 (m-10) cc_final: 0.8245 (m-80) REVERT: A 500 SER cc_start: 0.9036 (t) cc_final: 0.8403 (p) REVERT: A 510 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.7852 (m) REVERT: A 721 ASN cc_start: 0.8498 (m-40) cc_final: 0.8207 (t0) REVERT: A 838 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7657 (p0) REVERT: A 918 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 1001 ARG cc_start: 0.8049 (tpt170) cc_final: 0.7792 (tpt170) REVERT: B 37 MET cc_start: 0.8038 (mmm) cc_final: 0.7724 (mmm) REVERT: B 107 MET cc_start: 0.3455 (mmp) cc_final: 0.0575 (mtt) REVERT: B 151 MET cc_start: 0.2377 (ptt) cc_final: -0.0574 (ttt) REVERT: B 285 GLU cc_start: 0.8688 (tp30) cc_final: 0.8354 (tp30) REVERT: B 679 MET cc_start: 0.8567 (tpp) cc_final: 0.8083 (tpp) REVERT: B 721 ASN cc_start: 0.8284 (m-40) cc_final: 0.6913 (t0) REVERT: B 755 GLU cc_start: 0.8766 (tt0) cc_final: 0.8311 (tt0) REVERT: B 759 ASN cc_start: 0.8958 (m110) cc_final: 0.8204 (m110) REVERT: B 846 LEU cc_start: 0.8550 (tp) cc_final: 0.8291 (tp) REVERT: B 1013 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: C 101 TRP cc_start: 0.7479 (m-10) cc_final: 0.7270 (m-10) REVERT: C 184 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.6866 (pt0) REVERT: C 231 PHE cc_start: 0.8930 (p90) cc_final: 0.8434 (p90) REVERT: C 274 ASP cc_start: 0.7833 (t0) cc_final: 0.7567 (t0) REVERT: C 287 LYS cc_start: 0.9127 (mttt) cc_final: 0.8798 (mtpt) REVERT: C 528 ASN cc_start: 0.8010 (t0) cc_final: 0.7636 (t0) REVERT: C 558 PHE cc_start: 0.7375 (m-10) cc_final: 0.6941 (m-10) REVERT: C 868 TRP cc_start: 0.5565 (t60) cc_final: 0.5283 (t60) REVERT: C 972 GLU cc_start: 0.8607 (mp0) cc_final: 0.8086 (mp0) outliers start: 62 outliers final: 50 residues processed: 305 average time/residue: 0.3176 time to fit residues: 159.5000 Evaluate side-chains 280 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 225 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 0.0000 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.108518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.079089 restraints weight = 83484.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082760 restraints weight = 49714.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083722 restraints weight = 29516.960| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25433 Z= 0.241 Angle : 0.703 15.464 34613 Z= 0.365 Chirality : 0.047 0.280 3918 Planarity : 0.004 0.055 4485 Dihedral : 5.803 58.285 3422 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.31 % Favored : 87.46 % Rotamer: Outliers : 2.18 % Allowed : 14.79 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.51 (0.15), residues: 3159 helix: 1.15 (0.22), residues: 613 sheet: -1.08 (0.22), residues: 595 loop : -3.02 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 868 HIS 0.009 0.001 HIS C 181 PHE 0.037 0.002 PHE B 558 TYR 0.018 0.001 TYR C 88 ARG 0.006 0.000 ARG C 996 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4633.58 seconds wall clock time: 84 minutes 7.95 seconds (5047.95 seconds total)