Starting phenix.real_space_refine on Mon Feb 19 13:33:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/02_2024/6acd_9589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/02_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_9589/02_2024/6acd_9589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/02_2024/6acd_9589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/02_2024/6acd_9589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/02_2024/6acd_9589.pdb" } 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 Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1021": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1001": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1021": "NH1" <-> "NH2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1073": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.92, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.05 Conformation dependent library (CDL) restraints added in 4.4 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: 2.62 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: 9.35 Time building geometry restraints manager: 9.83 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: 98.06 - 105.26: 545 105.26 - 112.47: 12701 112.47 - 119.67: 8229 119.67 - 126.87: 12869 126.87 - 134.08: 269 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 2.440 nonbonded pdb=" O GLN C 939 " pdb=" OG1 THR C 943 " model vdw 2.246 2.440 nonbonded pdb=" OG SER C 95 " pdb=" O SER C 173 " model vdw 2.262 2.440 nonbonded pdb=" OG SER B 95 " pdb=" O SER B 173 " model vdw 2.281 2.440 ... (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 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: 1.860 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: 6.750 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 63.800 Find NCS groups from input model: 1.560 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.560 ------------------------------------------------------------------------------- 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 : 2.949 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: 0.4182 time to fit residues: 366.8939 Evaluate side-chains 297 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 2.970 ------------------------------------------------------------------------------- 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: 3.9990 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 0.0870 chunk 128 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 287 optimal weight: 3.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 699 ASN A 769 GLN A 931 GLN A 935 ASN A 984 GLN A 987 GLN A 993 GLN A1005 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 181 HIS B 445 HIS B 699 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN B 883 GLN B 937 ASN B1088 GLN B1101 ASN C 147 GLN C 181 HIS ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 759 ASN C 766 GLN C 947 GLN C 984 GLN C 987 GLN C 993 GLN C1005 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2538 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= 0.205 Angle : 0.708 10.483 34613 Z= 0.374 Chirality : 0.047 0.291 3918 Planarity : 0.005 0.058 4485 Dihedral : 6.827 63.839 3425 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.65 % Favored : 88.00 % Rotamer: Outliers : 2.25 % Allowed : 9.17 % Favored : 88.58 % 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: -3.56 (0.13), residues: 3159 helix: 0.02 (0.20), residues: 622 sheet: -1.73 (0.22), residues: 547 loop : -3.60 (0.11), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 423 HIS 0.010 0.001 HIS C1030 PHE 0.030 0.001 PHE B1085 TYR 0.018 0.001 TYR C 723 ARG 0.012 0.001 ARG B 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 424 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 362 time to evaluate : 2.893 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: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.9376 (mt) cc_final: 0.9036 (tp) REVERT: A 184 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7391 (mt-10) REVERT: A 245 TRP cc_start: 0.4259 (p-90) cc_final: 0.3142 (p-90) REVERT: A 253 PHE cc_start: 0.8706 (m-10) cc_final: 0.8366 (m-10) REVERT: A 361 PHE cc_start: 0.7259 (m-10) cc_final: 0.6927 (m-10) REVERT: A 423 TRP cc_start: 0.7953 (p90) cc_final: 0.7605 (p90) REVERT: A 439 LYS cc_start: 0.7441 (pttt) cc_final: 0.7181 (ptpt) REVERT: A 491 TYR cc_start: 0.8592 (m-10) cc_final: 0.8181 (m-80) REVERT: A 519 LEU cc_start: 0.8804 (mp) cc_final: 0.8221 (tt) REVERT: A 687 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8058 (tp) REVERT: A 840 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8753 (pp) REVERT: A 1024 PHE cc_start: 0.8184 (t80) cc_final: 0.7628 (t80) REVERT: B 87 ILE cc_start: 0.8796 (pt) cc_final: 0.8164 (mm) REVERT: B 107 MET cc_start: 0.2729 (mmp) cc_final: 0.0050 (mtt) REVERT: B 280 GLN cc_start: 0.8598 (tt0) cc_final: 0.8029 (tt0) REVERT: B 376 ASP cc_start: 0.7221 (t0) cc_final: 0.7003 (t0) REVERT: B 426 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6407 (tpp80) REVERT: B 918 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8362 (tp30) REVERT: C 184 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: C 274 ASP cc_start: 0.7617 (t0) cc_final: 0.7356 (t0) REVERT: C 287 LYS cc_start: 0.9418 (mttt) cc_final: 0.9122 (mttm) REVERT: C 528 ASN cc_start: 0.8464 (t0) cc_final: 0.7889 (t0) REVERT: C 538 LEU cc_start: 0.8770 (mt) cc_final: 0.8465 (mp) REVERT: C 947 GLN cc_start: 0.8479 (mm110) cc_final: 0.8093 (mp10) REVERT: C 1089 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7462 (mmm160) outliers start: 62 outliers final: 28 residues processed: 404 average time/residue: 0.3791 time to fit residues: 244.6376 Evaluate side-chains 299 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 2.853 ------------------------------------------------------------------------------- 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 535 THR Chi-restraints excluded: chain A residue 605 ASP 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 302 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 970 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 288 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 256 optimal weight: 50.0000 chunk 285 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 733 ASN A 917 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 505 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B1101 ASN C 304 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 942 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 25433 Z= 0.303 Angle : 0.727 10.091 34613 Z= 0.383 Chirality : 0.047 0.214 3918 Planarity : 0.005 0.061 4485 Dihedral : 6.595 65.751 3424 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.80 % Favored : 85.88 % Rotamer: Outliers : 3.26 % Allowed : 10.19 % Favored : 86.55 % 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: -3.25 (0.14), residues: 3159 helix: 0.62 (0.21), residues: 618 sheet: -1.58 (0.22), residues: 576 loop : -3.52 (0.12), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.010 0.001 HIS C1030 PHE 0.023 0.002 PHE B 379 TYR 0.020 0.001 TYR C 723 ARG 0.012 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 362 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 272 time to evaluate : 2.937 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: A 54 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9153 (tt) REVERT: A 245 TRP cc_start: 0.4424 (p-90) cc_final: 0.3466 (p-90) REVERT: A 393 ASP cc_start: 0.8709 (m-30) cc_final: 0.8375 (m-30) REVERT: A 423 TRP cc_start: 0.8086 (p90) cc_final: 0.7652 (p90) REVERT: A 491 TYR cc_start: 0.8656 (m-10) cc_final: 0.8228 (m-80) REVERT: A 502 GLU cc_start: 0.7145 (tt0) cc_final: 0.6645 (mt-10) REVERT: A 519 LEU cc_start: 0.8753 (mp) cc_final: 0.8142 (tt) REVERT: A 687 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 838 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7923 (p0) REVERT: A 882 MET cc_start: 0.8288 (mtp) cc_final: 0.7985 (mtp) REVERT: A 918 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 107 MET cc_start: 0.3033 (mmp) cc_final: 0.0210 (mtt) REVERT: B 151 MET cc_start: 0.3249 (ptm) cc_final: 0.2800 (ptt) REVERT: B 280 GLN cc_start: 0.8765 (tt0) cc_final: 0.8415 (tt0) REVERT: B 677 TYR cc_start: 0.7798 (p90) cc_final: 0.6981 (p90) REVERT: B 721 ASN cc_start: 0.8571 (m-40) cc_final: 0.8152 (t0) REVERT: B 918 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8477 (tp30) REVERT: B 1013 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 184 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6950 (pt0) REVERT: C 274 ASP cc_start: 0.7805 (t0) cc_final: 0.7513 (t0) REVERT: C 287 LYS cc_start: 0.9347 (mttt) cc_final: 0.9052 (mttm) REVERT: C 417 MET cc_start: -0.1268 (mmm) cc_final: -0.1511 (mmp) REVERT: C 528 ASN cc_start: 0.8610 (t0) cc_final: 0.8038 (t0) REVERT: C 538 LEU cc_start: 0.8804 (mt) cc_final: 0.8550 (mp) REVERT: C 947 GLN cc_start: 0.8683 (mm110) cc_final: 0.8297 (mp10) REVERT: C 1089 ARG cc_start: 0.7892 (ttt180) cc_final: 0.6902 (mmm-85) outliers start: 90 outliers final: 61 residues processed: 342 average time/residue: 0.3430 time to fit residues: 190.0204 Evaluate side-chains 302 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 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 191 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 ASP 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 801 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1012 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 302 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 863 THR 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 1012 SER Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 530 ASN 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 684 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1000 ILE 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: 5.9990 chunk 216 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 289 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 274 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 917 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25433 Z= 0.288 Angle : 0.708 9.888 34613 Z= 0.371 Chirality : 0.047 0.242 3918 Planarity : 0.005 0.061 4485 Dihedral : 6.480 64.948 3424 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.92 % Favored : 86.77 % Rotamer: Outliers : 3.48 % Allowed : 11.31 % Favored : 85.21 % 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: -3.06 (0.14), residues: 3159 helix: 0.99 (0.21), residues: 607 sheet: -1.58 (0.21), residues: 602 loop : -3.43 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 868 HIS 0.010 0.001 HIS C1030 PHE 0.033 0.002 PHE B 837 TYR 0.015 0.001 TYR C 723 ARG 0.010 0.001 ARG B 620 *********************** 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 348 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 252 time to evaluate : 2.832 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: A 54 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9167 (tt) REVERT: A 80 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 245 TRP cc_start: 0.4508 (p-90) cc_final: 0.3509 (p-90) REVERT: A 393 ASP cc_start: 0.8744 (m-30) cc_final: 0.8425 (m-30) REVERT: A 423 TRP cc_start: 0.8113 (p90) cc_final: 0.7709 (p90) REVERT: A 491 TYR cc_start: 0.8676 (m-10) cc_final: 0.8254 (m-80) REVERT: A 498 VAL cc_start: 0.9452 (t) cc_final: 0.9226 (p) REVERT: A 502 GLU cc_start: 0.7127 (tt0) cc_final: 0.6601 (mt-10) REVERT: A 687 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 721 ASN cc_start: 0.8748 (t0) cc_final: 0.8384 (t0) REVERT: A 741 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6971 (m-10) REVERT: A 838 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 882 MET cc_start: 0.8321 (mtp) cc_final: 0.7968 (mtp) REVERT: A 966 LEU cc_start: 0.8015 (pp) cc_final: 0.7642 (pp) REVERT: B 87 ILE cc_start: 0.8628 (pt) cc_final: 0.8294 (mt) REVERT: B 107 MET cc_start: 0.3239 (mmp) cc_final: 0.0382 (mtt) REVERT: B 285 GLU cc_start: 0.8449 (tp30) cc_final: 0.8102 (tp30) REVERT: B 679 MET cc_start: 0.8020 (tpp) cc_final: 0.7545 (tpp) REVERT: B 1013 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: C 184 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: C 231 PHE cc_start: 0.8890 (p90) cc_final: 0.8272 (p90) REVERT: C 274 ASP cc_start: 0.7918 (t0) cc_final: 0.7624 (t0) REVERT: C 287 LYS cc_start: 0.9292 (mttt) cc_final: 0.8948 (mtpt) REVERT: C 528 ASN cc_start: 0.8431 (t0) cc_final: 0.7850 (t0) REVERT: C 538 LEU cc_start: 0.8812 (mt) cc_final: 0.8594 (mp) REVERT: C 868 TRP cc_start: 0.5636 (t60) cc_final: 0.5407 (t60) REVERT: C 930 LEU cc_start: 0.9134 (mt) cc_final: 0.8881 (mp) REVERT: C 1089 ARG cc_start: 0.7510 (ttt90) cc_final: 0.7025 (mmm-85) outliers start: 96 outliers final: 60 residues processed: 326 average time/residue: 0.3207 time to fit residues: 172.4369 Evaluate side-chains 291 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 2.968 ------------------------------------------------------------------------------- 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 191 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 ASP 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 801 GLU 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 859 LEU Chi-restraints excluded: chain A residue 1012 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 302 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1012 SER 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 184 GLU Chi-restraints excluded: chain C residue 205 VAL 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 530 ASN Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 956 SER 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: 30.0000 chunk 173 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 409 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25433 Z= 0.324 Angle : 0.723 11.185 34613 Z= 0.379 Chirality : 0.047 0.186 3918 Planarity : 0.005 0.058 4485 Dihedral : 6.459 64.022 3424 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.43 % Favored : 85.25 % Rotamer: Outliers : 3.81 % Allowed : 11.42 % Favored : 84.77 % 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: -3.00 (0.14), residues: 3159 helix: 0.97 (0.21), residues: 612 sheet: -1.54 (0.22), residues: 570 loop : -3.35 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 868 HIS 0.010 0.001 HIS C1030 PHE 0.035 0.002 PHE B 837 TYR 0.015 0.002 TYR C 723 ARG 0.013 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 337 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 232 time to evaluate : 2.794 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: 0.9460 (OUTLIER) cc_final: 0.9174 (tt) REVERT: A 80 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 245 TRP cc_start: 0.5242 (p-90) cc_final: 0.4253 (p-90) REVERT: A 393 ASP cc_start: 0.8753 (m-30) cc_final: 0.8458 (m-30) REVERT: A 423 TRP cc_start: 0.8225 (p90) cc_final: 0.7811 (p90) REVERT: A 491 TYR cc_start: 0.8740 (m-10) cc_final: 0.8319 (m-80) REVERT: A 502 GLU cc_start: 0.7102 (tt0) cc_final: 0.6562 (mt-10) REVERT: A 687 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 838 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7779 (p0) REVERT: A 966 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7614 (pp) REVERT: B 151 MET cc_start: 0.2832 (OUTLIER) cc_final: 0.0349 (ttt) REVERT: B 679 MET cc_start: 0.8574 (tpp) cc_final: 0.7831 (tpp) REVERT: B 721 ASN cc_start: 0.8697 (m-40) cc_final: 0.8487 (t0) REVERT: B 762 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7711 (mp0) REVERT: B 1013 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: B 1101 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7393 (t0) REVERT: C 184 GLU cc_start: 0.8192 (tt0) cc_final: 0.7050 (pt0) REVERT: C 231 PHE cc_start: 0.8911 (p90) cc_final: 0.8185 (p90) REVERT: C 274 ASP cc_start: 0.8093 (t0) cc_final: 0.7778 (t0) REVERT: C 287 LYS cc_start: 0.9269 (mttt) cc_final: 0.8996 (mttm) REVERT: C 528 ASN cc_start: 0.8399 (t0) cc_final: 0.7903 (t0) REVERT: C 538 LEU cc_start: 0.8875 (mt) cc_final: 0.8647 (mp) REVERT: C 1032 MET cc_start: 0.7480 (tpp) cc_final: 0.7004 (tpp) outliers start: 105 outliers final: 75 residues processed: 314 average time/residue: 0.3346 time to fit residues: 174.2839 Evaluate side-chains 298 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 215 time to evaluate : 2.840 ------------------------------------------------------------------------------- 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 191 ASP 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 372 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 ASP 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 801 GLU 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 1012 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 87 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN 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 724 ILE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 902 GLN 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 1012 SER 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 B residue 1101 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 205 VAL 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 260 THR Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR 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 616 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1001 ARG 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: 0.9990 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 306 optimal weight: 0.7980 chunk 254 optimal weight: 0.0870 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 744 GLN A 759 ASN A 877 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25433 Z= 0.228 Angle : 0.673 10.086 34613 Z= 0.353 Chirality : 0.046 0.170 3918 Planarity : 0.004 0.069 4485 Dihedral : 6.218 61.772 3424 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.92 % Favored : 86.80 % Rotamer: Outliers : 3.48 % Allowed : 12.22 % Favored : 84.30 % 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: -2.86 (0.14), residues: 3159 helix: 1.05 (0.21), residues: 628 sheet: -1.51 (0.22), residues: 589 loop : -3.27 (0.12), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 868 HIS 0.009 0.001 HIS C1030 PHE 0.033 0.001 PHE B 837 TYR 0.013 0.001 TYR C 63 ARG 0.007 0.001 ARG C1089 *********************** 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 343 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 247 time to evaluate : 2.943 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: 0.9448 (OUTLIER) cc_final: 0.9194 (tt) REVERT: A 220 PHE cc_start: 0.8279 (m-10) cc_final: 0.7923 (m-10) REVERT: A 245 TRP cc_start: 0.5168 (p-90) cc_final: 0.4316 (p-90) REVERT: A 393 ASP cc_start: 0.8708 (m-30) cc_final: 0.8411 (m-30) REVERT: A 423 TRP cc_start: 0.8182 (p90) cc_final: 0.7774 (p90) REVERT: A 491 TYR cc_start: 0.8717 (m-10) cc_final: 0.8289 (m-80) REVERT: A 502 GLU cc_start: 0.6965 (tt0) cc_final: 0.6447 (mt-10) REVERT: A 838 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7635 (p0) REVERT: A 966 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7483 (pp) REVERT: A 1011 MET cc_start: 0.8130 (tpp) cc_final: 0.7886 (tpt) REVERT: B 87 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 107 MET cc_start: 0.3872 (mmp) cc_final: 0.1079 (mtt) REVERT: B 151 MET cc_start: 0.2866 (ptm) cc_final: 0.0239 (ttt) REVERT: B 285 GLU cc_start: 0.8617 (tp30) cc_final: 0.8328 (tp30) REVERT: B 601 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 679 MET cc_start: 0.8608 (tpp) cc_final: 0.7956 (tpp) REVERT: B 762 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7625 (mp0) REVERT: B 1013 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: B 1101 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.6949 (t0) REVERT: C 184 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6903 (pt0) REVERT: C 231 PHE cc_start: 0.8832 (p90) cc_final: 0.8093 (p90) REVERT: C 274 ASP cc_start: 0.8052 (t0) cc_final: 0.7713 (t0) REVERT: C 287 LYS cc_start: 0.9239 (mttt) cc_final: 0.8871 (mtpt) REVERT: C 528 ASN cc_start: 0.8496 (t0) cc_final: 0.7917 (t0) REVERT: C 538 LEU cc_start: 0.8956 (mt) cc_final: 0.8755 (mp) REVERT: C 868 TRP cc_start: 0.5689 (t60) cc_final: 0.5218 (t60) REVERT: C 948 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8986 (mt) REVERT: C 1032 MET cc_start: 0.7577 (tpp) cc_final: 0.7168 (tpp) outliers start: 96 outliers final: 64 residues processed: 323 average time/residue: 0.3130 time to fit residues: 168.4142 Evaluate side-chains 291 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 218 time to evaluate : 2.708 ------------------------------------------------------------------------------- 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 191 ASP 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 510 VAL Chi-restraints excluded: chain A residue 605 ASP 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 801 GLU 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 1012 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 66 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 601 VAL 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 724 ILE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1101 ASN 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 205 VAL 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 260 THR Chi-restraints excluded: chain C residue 530 ASN 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 687 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1001 ARG 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: 0.9990 chunk 34 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 258 optimal weight: 30.0000 chunk 171 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25433 Z= 0.332 Angle : 0.732 13.576 34613 Z= 0.383 Chirality : 0.046 0.206 3918 Planarity : 0.005 0.061 4485 Dihedral : 6.302 60.077 3422 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.04 % Favored : 84.71 % Rotamer: Outliers : 3.92 % Allowed : 12.69 % Favored : 83.39 % 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: -2.92 (0.14), residues: 3159 helix: 1.02 (0.21), residues: 612 sheet: -1.54 (0.22), residues: 587 loop : -3.28 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 868 HIS 0.013 0.001 HIS C1030 PHE 0.041 0.002 PHE B 837 TYR 0.019 0.001 TYR B 899 ARG 0.008 0.001 ARG A 758 *********************** 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 325 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 217 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9208 (tt) REVERT: A 220 PHE cc_start: 0.8271 (m-10) cc_final: 0.7876 (m-10) REVERT: A 245 TRP cc_start: 0.5276 (p-90) cc_final: 0.4541 (p-90) REVERT: A 253 PHE cc_start: 0.8685 (m-10) cc_final: 0.8434 (m-10) REVERT: A 393 ASP cc_start: 0.8774 (m-30) cc_final: 0.8528 (m-30) REVERT: A 423 TRP cc_start: 0.8111 (p90) cc_final: 0.7686 (p90) REVERT: A 436 TYR cc_start: 0.8058 (m-10) cc_final: 0.7852 (m-10) REVERT: A 491 TYR cc_start: 0.8724 (m-10) cc_final: 0.8318 (m-80) REVERT: A 502 GLU cc_start: 0.7027 (tt0) cc_final: 0.6543 (mt-10) REVERT: A 510 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8418 (m) REVERT: A 721 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8198 (t0) REVERT: A 838 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 1011 MET cc_start: 0.8216 (tpp) cc_final: 0.7780 (tpp) REVERT: B 151 MET cc_start: 0.3043 (ptm) cc_final: 0.0470 (ttt) REVERT: B 285 GLU cc_start: 0.8598 (tp30) cc_final: 0.8325 (tp30) REVERT: B 601 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8330 (t) REVERT: B 679 MET cc_start: 0.8783 (tpp) cc_final: 0.8090 (tpp) REVERT: B 741 PHE cc_start: 0.7233 (t80) cc_final: 0.6982 (t80) REVERT: B 762 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7608 (mp0) REVERT: B 1013 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: C 184 GLU cc_start: 0.8096 (tt0) cc_final: 0.6960 (pt0) REVERT: C 231 PHE cc_start: 0.8943 (p90) cc_final: 0.8140 (p90) REVERT: C 274 ASP cc_start: 0.8070 (t0) cc_final: 0.7766 (t0) REVERT: C 287 LYS cc_start: 0.9233 (mttt) cc_final: 0.8959 (mttm) REVERT: C 528 ASN cc_start: 0.8468 (t0) cc_final: 0.7898 (t0) REVERT: C 868 TRP cc_start: 0.5649 (t60) cc_final: 0.5426 (t60) REVERT: C 948 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9000 (mt) REVERT: C 1032 MET cc_start: 0.7731 (tpp) cc_final: 0.7235 (tpp) REVERT: C 1070 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8500 (m-10) outliers start: 108 outliers final: 78 residues processed: 304 average time/residue: 0.3124 time to fit residues: 159.0439 Evaluate side-chains 292 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 206 time to evaluate : 2.772 ------------------------------------------------------------------------------- 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 191 ASP 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 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 ASP 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 1012 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 230 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 601 VAL 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 724 ILE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 863 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 1012 SER Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1074 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 205 VAL 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 260 THR Chi-restraints excluded: chain C residue 530 ASN 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 616 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1070 TYR 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: 1.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25433 Z= 0.228 Angle : 0.680 10.524 34613 Z= 0.355 Chirality : 0.046 0.281 3918 Planarity : 0.004 0.057 4485 Dihedral : 6.122 59.453 3422 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.92 % Favored : 86.83 % Rotamer: Outliers : 3.37 % Allowed : 13.13 % Favored : 83.50 % 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: -2.77 (0.15), residues: 3159 helix: 1.18 (0.22), residues: 604 sheet: -1.48 (0.22), residues: 597 loop : -3.18 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 868 HIS 0.010 0.001 HIS C1030 PHE 0.038 0.001 PHE B 837 TYR 0.014 0.001 TYR C 63 ARG 0.005 0.000 ARG C1089 *********************** 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 319 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 226 time to evaluate : 2.747 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: 0.9465 (OUTLIER) cc_final: 0.9192 (tt) REVERT: A 220 PHE cc_start: 0.8200 (m-10) cc_final: 0.7782 (m-10) REVERT: A 393 ASP cc_start: 0.8763 (m-30) cc_final: 0.8503 (m-30) REVERT: A 423 TRP cc_start: 0.8096 (p90) cc_final: 0.7669 (p90) REVERT: A 491 TYR cc_start: 0.8726 (m-10) cc_final: 0.8283 (m-80) REVERT: A 502 GLU cc_start: 0.6922 (tt0) cc_final: 0.6432 (mt-10) REVERT: A 510 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8293 (m) REVERT: A 838 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7596 (p0) REVERT: B 37 MET cc_start: 0.8381 (mmm) cc_final: 0.7815 (mmm) REVERT: B 107 MET cc_start: 0.3805 (mmp) cc_final: 0.0825 (mtt) REVERT: B 151 MET cc_start: 0.3160 (ptm) cc_final: 0.0905 (ttt) REVERT: B 601 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8349 (t) REVERT: B 679 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8113 (tpp) REVERT: B 738 TYR cc_start: 0.7956 (m-10) cc_final: 0.7447 (m-80) REVERT: B 741 PHE cc_start: 0.6825 (t80) cc_final: 0.6414 (t80) REVERT: B 745 LEU cc_start: 0.9330 (mp) cc_final: 0.9085 (mp) REVERT: B 755 GLU cc_start: 0.8852 (tt0) cc_final: 0.8623 (tt0) REVERT: B 762 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7586 (mp0) REVERT: B 1013 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: C 184 GLU cc_start: 0.8168 (tt0) cc_final: 0.7000 (pt0) REVERT: C 231 PHE cc_start: 0.8933 (p90) cc_final: 0.8142 (p90) REVERT: C 274 ASP cc_start: 0.7997 (t0) cc_final: 0.7674 (t0) REVERT: C 287 LYS cc_start: 0.9174 (mttt) cc_final: 0.8837 (mtpt) REVERT: C 528 ASN cc_start: 0.8433 (t0) cc_final: 0.7868 (t0) REVERT: C 1011 MET cc_start: 0.8547 (tpp) cc_final: 0.8292 (tpp) REVERT: C 1032 MET cc_start: 0.7518 (tpp) cc_final: 0.7103 (tpp) outliers start: 93 outliers final: 75 residues processed: 301 average time/residue: 0.3091 time to fit residues: 155.5323 Evaluate side-chains 295 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 214 time to evaluate : 2.560 ------------------------------------------------------------------------------- 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 191 ASP 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 318 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP 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 768 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 ASP 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 1097 ILE 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 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 601 VAL 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 724 ILE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1058 THR 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 205 VAL 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 260 THR Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 530 ASN 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 616 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 863 THR 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: 0.9990 chunk 292 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25433 Z= 0.290 Angle : 0.715 10.096 34613 Z= 0.373 Chirality : 0.046 0.256 3918 Planarity : 0.005 0.056 4485 Dihedral : 6.181 59.394 3422 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.85 % Favored : 84.90 % Rotamer: Outliers : 3.41 % Allowed : 13.42 % Favored : 83.18 % 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: -2.85 (0.15), residues: 3159 helix: 0.99 (0.21), residues: 622 sheet: -1.46 (0.22), residues: 589 loop : -3.23 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 868 HIS 0.011 0.001 HIS C1030 PHE 0.036 0.002 PHE B 837 TYR 0.018 0.001 TYR C 723 ARG 0.006 0.001 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 309 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 215 time to evaluate : 2.886 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: A 54 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9194 (tt) REVERT: A 220 PHE cc_start: 0.8225 (m-10) cc_final: 0.7801 (m-10) REVERT: A 245 TRP cc_start: 0.5392 (p-90) cc_final: 0.4766 (p-90) REVERT: A 393 ASP cc_start: 0.8774 (m-30) cc_final: 0.8254 (m-30) REVERT: A 423 TRP cc_start: 0.8108 (p90) cc_final: 0.7651 (p90) REVERT: A 491 TYR cc_start: 0.8732 (m-10) cc_final: 0.8285 (m-80) REVERT: A 502 GLU cc_start: 0.6997 (tt0) cc_final: 0.6495 (mt-10) REVERT: A 838 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7599 (p0) REVERT: B 37 MET cc_start: 0.8398 (mmm) cc_final: 0.7881 (mmm) REVERT: B 151 MET cc_start: 0.3584 (ptm) cc_final: 0.1490 (ttt) REVERT: B 285 GLU cc_start: 0.8722 (tp30) cc_final: 0.8449 (tp30) REVERT: B 601 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (t) REVERT: B 679 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8156 (tpp) REVERT: B 755 GLU cc_start: 0.8843 (tt0) cc_final: 0.8611 (tt0) REVERT: B 762 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 1013 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: C 184 GLU cc_start: 0.8096 (tt0) cc_final: 0.6940 (pt0) REVERT: C 231 PHE cc_start: 0.9038 (p90) cc_final: 0.8396 (p90) REVERT: C 274 ASP cc_start: 0.7717 (t0) cc_final: 0.7424 (t0) REVERT: C 287 LYS cc_start: 0.9196 (mttt) cc_final: 0.8857 (mtpt) REVERT: C 528 ASN cc_start: 0.8465 (t0) cc_final: 0.7924 (t0) REVERT: C 939 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8004 (tp40) REVERT: C 1032 MET cc_start: 0.7742 (tpp) cc_final: 0.7268 (tpp) outliers start: 94 outliers final: 80 residues processed: 290 average time/residue: 0.3163 time to fit residues: 152.4725 Evaluate side-chains 293 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 207 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 191 ASP 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 318 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP 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 762 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 ASP 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 1097 ILE 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 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 601 VAL 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 724 ILE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 863 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 1012 SER Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1058 THR 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 205 VAL 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 530 ASN Chi-restraints excluded: chain C residue 535 THR 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 616 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 939 GLN Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1001 ARG 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: 0.8980 chunk 301 optimal weight: 0.9980 chunk 183 optimal weight: 0.0470 chunk 142 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 315 optimal weight: 0.0020 chunk 290 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.5686 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25433 Z= 0.177 Angle : 0.669 10.385 34613 Z= 0.347 Chirality : 0.046 0.252 3918 Planarity : 0.004 0.059 4485 Dihedral : 5.865 58.012 3422 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.78 % Favored : 87.97 % Rotamer: Outliers : 2.36 % Allowed : 14.58 % Favored : 83.07 % 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: -2.62 (0.15), residues: 3159 helix: 1.21 (0.22), residues: 616 sheet: -1.30 (0.21), residues: 624 loop : -3.11 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 868 HIS 0.008 0.001 HIS C1030 PHE 0.028 0.001 PHE B 837 TYR 0.017 0.001 TYR C 723 ARG 0.005 0.000 ARG C1089 ********************** 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 325 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 260 time to evaluate : 3.012 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 220 PHE cc_start: 0.8166 (m-10) cc_final: 0.7745 (m-10) REVERT: A 245 TRP cc_start: 0.4940 (p-90) cc_final: 0.4716 (p-90) REVERT: A 393 ASP cc_start: 0.8439 (m-30) cc_final: 0.8142 (m-30) REVERT: A 423 TRP cc_start: 0.8060 (p90) cc_final: 0.7589 (p90) REVERT: A 491 TYR cc_start: 0.8722 (m-10) cc_final: 0.8271 (m-80) REVERT: A 500 SER cc_start: 0.9315 (t) cc_final: 0.8677 (p) REVERT: A 502 GLU cc_start: 0.6785 (tt0) cc_final: 0.6387 (mt-10) REVERT: A 838 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7526 (p0) REVERT: A 841 THR cc_start: 0.9165 (t) cc_final: 0.8890 (m) REVERT: A 984 GLN cc_start: 0.8333 (mm110) cc_final: 0.7818 (tp40) REVERT: B 37 MET cc_start: 0.8210 (mmm) cc_final: 0.7705 (mmm) REVERT: B 107 MET cc_start: 0.4044 (mmp) cc_final: 0.1308 (mtt) REVERT: B 151 MET cc_start: 0.3256 (ptm) cc_final: 0.1238 (ttt) REVERT: B 285 GLU cc_start: 0.8712 (tp30) cc_final: 0.8466 (tp30) REVERT: B 679 MET cc_start: 0.8776 (tpp) cc_final: 0.8303 (tpp) REVERT: B 762 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7328 (mt-10) REVERT: B 846 LEU cc_start: 0.8147 (tp) cc_final: 0.7931 (tp) REVERT: B 984 GLN cc_start: 0.8281 (tt0) cc_final: 0.7998 (tt0) REVERT: C 184 GLU cc_start: 0.8176 (tt0) cc_final: 0.6874 (pt0) REVERT: C 220 PHE cc_start: 0.8052 (m-80) cc_final: 0.7787 (m-80) REVERT: C 231 PHE cc_start: 0.9032 (p90) cc_final: 0.8443 (p90) REVERT: C 274 ASP cc_start: 0.8007 (t0) cc_final: 0.7643 (t0) REVERT: C 287 LYS cc_start: 0.9121 (mttt) cc_final: 0.8762 (mtpt) REVERT: C 528 ASN cc_start: 0.8288 (t0) cc_final: 0.7813 (t0) REVERT: C 558 PHE cc_start: 0.7562 (m-10) cc_final: 0.7076 (m-10) REVERT: C 741 PHE cc_start: 0.7193 (m-80) cc_final: 0.6650 (m-80) REVERT: C 755 GLU cc_start: 0.7795 (pt0) cc_final: 0.7403 (pt0) REVERT: C 868 TRP cc_start: 0.5474 (t60) cc_final: 0.5180 (t60) REVERT: C 1032 MET cc_start: 0.7522 (tpp) cc_final: 0.7133 (tpp) outliers start: 65 outliers final: 57 residues processed: 313 average time/residue: 0.3409 time to fit residues: 179.3533 Evaluate side-chains 288 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.774 ------------------------------------------------------------------------------- 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 191 ASP 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 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP 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 801 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 ASP 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 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 530 ASN 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 706 THR Chi-restraints excluded: chain B residue 841 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 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 205 VAL 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 530 ASN 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 616 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 956 SER 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: 0.6980 chunk 267 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 69 optimal weight: 7.9990 chunk 251 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 258 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.112902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.087197 restraints weight = 87892.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.088351 restraints weight = 57207.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.089410 restraints weight = 40062.940| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25433 Z= 0.264 Angle : 0.701 14.206 34613 Z= 0.364 Chirality : 0.047 0.353 3918 Planarity : 0.004 0.056 4485 Dihedral : 5.929 58.382 3422 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.68 % Favored : 86.04 % Rotamer: Outliers : 2.47 % Allowed : 15.26 % Favored : 82.27 % 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: -2.61 (0.15), residues: 3159 helix: 1.27 (0.22), residues: 615 sheet: -1.27 (0.22), residues: 619 loop : -3.13 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 423 HIS 0.010 0.001 HIS C1030 PHE 0.037 0.002 PHE B 220 TYR 0.018 0.001 TYR C 723 ARG 0.005 0.000 ARG B 620 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4673.84 seconds wall clock time: 86 minutes 33.30 seconds (5193.30 seconds total)