Starting phenix.real_space_refine on Tue Mar 19 02:44:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/03_2024/6nd0_0439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/03_2024/6nd0_0439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/03_2024/6nd0_0439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/03_2024/6nd0_0439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/03_2024/6nd0_0439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/03_2024/6nd0_0439.pdb" } resolution = 3.5 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= 0.000 sd= 0.004 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 156 5.16 5 C 14736 2.51 5 N 3792 2.21 5 O 4280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1034": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1034": "NH1" <-> "NH2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ARG 393": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "D PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 575": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D ARG 1034": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Chain: "C" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Chain: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Time building chain proxies: 11.17, per 1000 atoms: 0.49 Number of scatterers: 22964 At special positions: 0 Unit cell: (140.448, 140.448, 130.944, 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 156 16.00 O 4280 8.00 N 3792 7.00 C 14736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 8.79 Conformation dependent library (CDL) restraints added in 4.3 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5504 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 18 sheets defined 42.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 229 through 260 removed outlier: 4.343A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.296A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 322 removed outlier: 4.213A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 353 through 364 removed outlier: 4.342A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.894A pdb=" N VAL A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.582A pdb=" N TYR A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.534A pdb=" N GLY A 480 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 498 removed outlier: 3.747A pdb=" N ALA A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.550A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.524A pdb=" N PHE A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.598A pdb=" N ALA A 608 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 798 through 801 removed outlier: 3.670A pdb=" N ALA A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 805 through 809 removed outlier: 3.878A pdb=" N LEU A 809 " --> pdb=" O TYR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 removed outlier: 4.680A pdb=" N ARG A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 850 removed outlier: 3.589A pdb=" N ALA A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.555A pdb=" N CYS A 855 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.615A pdb=" N ILE A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 950 removed outlier: 3.613A pdb=" N GLN A 947 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 949 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 950 " --> pdb=" O GLN A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 980 through 988 removed outlier: 3.777A pdb=" N PHE A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 992 removed outlier: 3.847A pdb=" N LEU A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 989 through 992' Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.894A pdb=" N THR A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1014 removed outlier: 3.831A pdb=" N LEU A1010 " --> pdb=" O GLU A1006 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1029 Processing helix chain 'A' and resid 1042 through 1046 removed outlier: 4.136A pdb=" N PHE A1045 " --> pdb=" O ASP A1042 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1046 " --> pdb=" O GLY A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1042 through 1046' Processing helix chain 'A' and resid 1053 through 1065 removed outlier: 3.662A pdb=" N CYS A1059 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1062 " --> pdb=" O PHE A1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 260 removed outlier: 4.344A pdb=" N LEU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.296A pdb=" N TYR B 279 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 322 removed outlier: 4.212A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 353 through 364 removed outlier: 4.342A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.894A pdb=" N VAL B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.583A pdb=" N TYR B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.534A pdb=" N GLY B 480 " --> pdb=" O TRP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 498 removed outlier: 3.746A pdb=" N ALA B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.550A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.525A pdb=" N PHE B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.599A pdb=" N ALA B 608 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 771 Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 798 through 801 removed outlier: 3.669A pdb=" N ALA B 801 " --> pdb=" O PRO B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 798 through 801' Processing helix chain 'B' and resid 805 through 809 removed outlier: 3.878A pdb=" N LEU B 809 " --> pdb=" O TYR B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 removed outlier: 4.680A pdb=" N ARG B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 824 " --> pdb=" O TYR B 820 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU B 826 " --> pdb=" O LYS B 822 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR B 827 " --> pdb=" O ARG B 823 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 828 " --> pdb=" O GLU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 850 removed outlier: 3.589A pdb=" N ALA B 849 " --> pdb=" O ALA B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.555A pdb=" N CYS B 855 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 886 removed outlier: 3.616A pdb=" N ILE B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 950 removed outlier: 3.613A pdb=" N GLN B 947 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 949 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 950 " --> pdb=" O GLN B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 969 Processing helix chain 'B' and resid 976 through 979 Processing helix chain 'B' and resid 980 through 988 removed outlier: 3.777A pdb=" N PHE B 987 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 988 " --> pdb=" O ALA B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1001 removed outlier: 3.675A pdb=" N ILE B 995 " --> pdb=" O ILE B 991 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1014 removed outlier: 3.832A pdb=" N LEU B1010 " --> pdb=" O GLU B1006 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B1014 " --> pdb=" O LEU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1029 Processing helix chain 'B' and resid 1042 through 1046 removed outlier: 4.137A pdb=" N PHE B1045 " --> pdb=" O ASP B1042 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B1046 " --> pdb=" O GLY B1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1042 through 1046' Processing helix chain 'B' and resid 1053 through 1065 removed outlier: 3.663A pdb=" N CYS B1059 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B1062 " --> pdb=" O PHE B1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.903A pdb=" N LEU C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 250 " --> pdb=" O TRP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 273 through 286 removed outlier: 4.089A pdb=" N CYS C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 279 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.904A pdb=" N MET C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.517A pdb=" N ILE C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.643A pdb=" N VAL C 356 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 removed outlier: 3.615A pdb=" N LEU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 449 removed outlier: 3.556A pdb=" N ASP C 437 " --> pdb=" O PRO C 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 447 " --> pdb=" O ARG C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.847A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 472 " --> pdb=" O HIS C 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 467 through 472' Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.647A pdb=" N GLY C 480 " --> pdb=" O TRP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 498 removed outlier: 3.622A pdb=" N LEU C 489 " --> pdb=" O CYS C 485 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.502A pdb=" N TYR C 528 " --> pdb=" O TRP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.615A pdb=" N PHE C 545 " --> pdb=" O SER C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 560 removed outlier: 3.532A pdb=" N GLU C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 556 " --> pdb=" O THR C 552 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 558 " --> pdb=" O CYS C 554 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 559 " --> pdb=" O GLU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 609 removed outlier: 3.649A pdb=" N LYS C 606 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.571A pdb=" N ILE C 762 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 771 removed outlier: 3.592A pdb=" N MET C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 798 through 800 No H-bonds generated for 'chain 'C' and resid 798 through 800' Processing helix chain 'C' and resid 817 through 825 removed outlier: 4.483A pdb=" N ARG C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 824 " --> pdb=" O TYR C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 828 No H-bonds generated for 'chain 'C' and resid 826 through 828' Processing helix chain 'C' and resid 843 through 850 removed outlier: 3.546A pdb=" N VAL C 850 " --> pdb=" O ASP C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 Processing helix chain 'C' and resid 875 through 886 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.783A pdb=" N ASN C 945 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN C 947 " --> pdb=" O THR C 944 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 950 " --> pdb=" O GLN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 969 removed outlier: 3.506A pdb=" N ALA C 968 " --> pdb=" O THR C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 979 Processing helix chain 'C' and resid 980 through 988 removed outlier: 3.594A pdb=" N PHE C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 996 removed outlier: 3.717A pdb=" N THR C 993 " --> pdb=" O ASP C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1013 removed outlier: 3.611A pdb=" N LEU C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1050 removed outlier: 4.333A pdb=" N ASP C1050 " --> pdb=" O ALA C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1065 removed outlier: 3.767A pdb=" N CYS C1059 " --> pdb=" O GLY C1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 252 removed outlier: 3.904A pdb=" N LEU D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 250 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 273 through 286 removed outlier: 4.088A pdb=" N CYS D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 279 " --> pdb=" O TRP D 275 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 316 removed outlier: 3.903A pdb=" N MET D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 305 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.517A pdb=" N ILE D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 removed outlier: 3.643A pdb=" N VAL D 356 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 removed outlier: 3.615A pdb=" N LEU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 449 removed outlier: 3.554A pdb=" N ASP D 437 " --> pdb=" O PRO D 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 447 " --> pdb=" O ARG D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 466 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.848A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 472 " --> pdb=" O HIS D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 467 through 472' Processing helix chain 'D' and resid 476 through 480 removed outlier: 3.647A pdb=" N GLY D 480 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 498 removed outlier: 3.623A pdb=" N LEU D 489 " --> pdb=" O CYS D 485 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 491 " --> pdb=" O ALA D 487 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 524 through 529 removed outlier: 3.502A pdb=" N TYR D 528 " --> pdb=" O TRP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.615A pdb=" N PHE D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 560 removed outlier: 3.533A pdb=" N GLU D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU D 556 " --> pdb=" O THR D 552 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 558 " --> pdb=" O CYS D 554 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 559 " --> pdb=" O GLU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 609 removed outlier: 3.650A pdb=" N LYS D 606 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 762 removed outlier: 3.571A pdb=" N ILE D 762 " --> pdb=" O GLU D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 771 removed outlier: 3.592A pdb=" N MET D 770 " --> pdb=" O SER D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 Processing helix chain 'D' and resid 798 through 800 No H-bonds generated for 'chain 'D' and resid 798 through 800' Processing helix chain 'D' and resid 817 through 825 removed outlier: 4.482A pdb=" N ARG D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 824 " --> pdb=" O TYR D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 828 No H-bonds generated for 'chain 'D' and resid 826 through 828' Processing helix chain 'D' and resid 843 through 850 removed outlier: 3.546A pdb=" N VAL D 850 " --> pdb=" O ASP D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 855 Processing helix chain 'D' and resid 875 through 886 Processing helix chain 'D' and resid 942 through 950 removed outlier: 3.783A pdb=" N ASN D 945 " --> pdb=" O ASN D 942 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 947 " --> pdb=" O THR D 944 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 950 " --> pdb=" O GLN D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 969 removed outlier: 3.506A pdb=" N ALA D 968 " --> pdb=" O THR D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 979 Processing helix chain 'D' and resid 980 through 988 removed outlier: 3.594A pdb=" N PHE D 987 " --> pdb=" O SER D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 996 removed outlier: 3.718A pdb=" N THR D 993 " --> pdb=" O ASP D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1013 removed outlier: 3.611A pdb=" N LEU D1010 " --> pdb=" O GLU D1006 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D1013 " --> pdb=" O ALA D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1050 removed outlier: 4.333A pdb=" N ASP D1050 " --> pdb=" O ALA D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1065 removed outlier: 3.767A pdb=" N CYS D1059 " --> pdb=" O GLY D1055 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.252A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.785A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 744 through 745 removed outlier: 4.483A pdb=" N TYR A 744 " --> pdb=" O GLY A1020 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A1020 " --> pdb=" O TYR A 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 834 through 838 removed outlier: 6.352A pdb=" N ILE A 812 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 837 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE A 814 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 782 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER A 862 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE A 973 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR A 938 " --> pdb=" O PHE A 973 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1036 through 1039 removed outlier: 3.599A pdb=" N ALA A1036 " --> pdb=" O CYS A1109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A1106 " --> pdb=" O TYR A1073 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A1071 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 398 through 399 removed outlier: 7.252A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 535 through 540 removed outlier: 3.784A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 744 through 745 removed outlier: 4.483A pdb=" N TYR B 744 " --> pdb=" O GLY B1020 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B1020 " --> pdb=" O TYR B 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 834 through 838 removed outlier: 6.352A pdb=" N ILE B 812 " --> pdb=" O SER B 835 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU B 837 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE B 814 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 782 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER B 862 " --> pdb=" O GLU B 939 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE B 973 " --> pdb=" O ILE B 936 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR B 938 " --> pdb=" O PHE B 973 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1036 through 1039 removed outlier: 3.599A pdb=" N ALA B1036 " --> pdb=" O CYS B1109 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B1106 " --> pdb=" O TYR B1073 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B1071 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 398 through 401 removed outlier: 4.059A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.166A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 834 through 838 removed outlier: 6.126A pdb=" N ILE C 812 " --> pdb=" O SER C 835 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C 837 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE C 814 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 777 " --> pdb=" O VAL C 813 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 815 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 779 " --> pdb=" O VAL C 815 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER C 862 " --> pdb=" O GLU C 939 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE C 973 " --> pdb=" O ILE C 936 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 938 " --> pdb=" O PHE C 973 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1036 through 1039 removed outlier: 3.976A pdb=" N ALA C1036 " --> pdb=" O CYS C1109 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C1071 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 398 through 401 removed outlier: 4.059A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.167A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 834 through 838 removed outlier: 6.127A pdb=" N ILE D 812 " --> pdb=" O SER D 835 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU D 837 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE D 814 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL D 777 " --> pdb=" O VAL D 813 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL D 815 " --> pdb=" O VAL D 777 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 779 " --> pdb=" O VAL D 815 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER D 862 " --> pdb=" O GLU D 939 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE D 973 " --> pdb=" O ILE D 936 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 938 " --> pdb=" O PHE D 973 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1036 through 1039 removed outlier: 3.976A pdb=" N ALA D1036 " --> pdb=" O CYS D1109 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D1071 " --> pdb=" O PHE D1108 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1779 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: 7.26 Time building geometry restraints manager: 9.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7242 1.34 - 1.46: 4472 1.46 - 1.57: 11514 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 23452 Sorted by residual: bond pdb=" CB ASN B 803 " pdb=" CG ASN B 803 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" CB ASN A 803 " pdb=" CG ASN A 803 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" C VAL A1102 " pdb=" N PRO A1103 " ideal model delta sigma weight residual 1.337 1.354 -0.017 9.80e-03 1.04e+04 3.17e+00 bond pdb=" C VAL B1102 " pdb=" N PRO B1103 " ideal model delta sigma weight residual 1.337 1.354 -0.017 9.80e-03 1.04e+04 3.17e+00 bond pdb=" CB VAL D 999 " pdb=" CG1 VAL D 999 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 ... (remaining 23447 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.45: 384 105.45 - 112.62: 12154 112.62 - 119.78: 8386 119.78 - 126.94: 10633 126.94 - 134.10: 259 Bond angle restraints: 31816 Sorted by residual: angle pdb=" C ASP C 745 " pdb=" N SER C 746 " pdb=" CA SER C 746 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C ASP D 745 " pdb=" N SER D 746 " pdb=" CA SER D 746 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LEU C1041 " pdb=" N ASP C1042 " pdb=" CA ASP C1042 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C LEU D1041 " pdb=" N ASP D1042 " pdb=" CA ASP D1042 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N SER C 746 " pdb=" CA SER C 746 " pdb=" C SER C 746 " ideal model delta sigma weight residual 110.80 119.90 -9.10 2.13e+00 2.20e-01 1.82e+01 ... (remaining 31811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 13293 17.30 - 34.60: 587 34.60 - 51.89: 81 51.89 - 69.19: 15 69.19 - 86.49: 12 Dihedral angle restraints: 13988 sinusoidal: 5476 harmonic: 8512 Sorted by residual: dihedral pdb=" CA GLU D 960 " pdb=" C GLU D 960 " pdb=" N LEU D 961 " pdb=" CA LEU D 961 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLU C 960 " pdb=" C GLU C 960 " pdb=" N LEU C 961 " pdb=" CA LEU C 961 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA CYS D1069 " pdb=" C CYS D1069 " pdb=" N PHE D1070 " pdb=" CA PHE D1070 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 13985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2529 0.056 - 0.112: 921 0.112 - 0.168: 169 0.168 - 0.224: 33 0.224 - 0.281: 8 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CB ILE A 579 " pdb=" CA ILE A 579 " pdb=" CG1 ILE A 579 " pdb=" CG2 ILE A 579 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE B 416 " pdb=" CA ILE B 416 " pdb=" CG1 ILE B 416 " pdb=" CG2 ILE B 416 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3657 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO B 320 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 320 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C PHE A1099 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A1100 " -0.014 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1355 2.72 - 3.27: 22519 3.27 - 3.81: 36671 3.81 - 4.36: 46195 4.36 - 4.90: 77456 Nonbonded interactions: 184196 Sorted by model distance: nonbonded pdb=" O TYR C 744 " pdb=" OD1 ASP C 745 " model vdw 2.178 3.040 nonbonded pdb=" O TYR D 744 " pdb=" OD1 ASP D 745 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR B 336 " pdb=" OE1 GLU B 374 " model vdw 2.274 2.440 nonbonded pdb=" OH TYR A 336 " pdb=" OE1 GLU A 374 " model vdw 2.274 2.440 nonbonded pdb=" O GLY B 531 " pdb=" OG1 THR B1093 " model vdw 2.275 2.440 ... (remaining 184191 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.870 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 57.400 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 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 : 0.008 0.077 23452 Z= 0.545 Angle : 0.939 9.717 31816 Z= 0.506 Chirality : 0.059 0.281 3660 Planarity : 0.006 0.062 4040 Dihedral : 10.798 86.490 8484 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.96 % Rotamer: Outliers : 0.43 % Allowed : 3.61 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.13), residues: 2884 helix: -4.36 (0.08), residues: 1022 sheet: -2.08 (0.24), residues: 388 loop : -2.29 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP D 825 HIS 0.010 0.002 HIS A 451 PHE 0.031 0.003 PHE D1070 TYR 0.038 0.003 TYR B1073 ARG 0.012 0.001 ARG A1076 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 533 time to evaluate : 2.205 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 238 LEU cc_start: 0.7180 (mt) cc_final: 0.6863 (mm) REVERT: A 242 PHE cc_start: 0.8382 (m-80) cc_final: 0.7819 (m-80) REVERT: A 279 TYR cc_start: 0.6537 (t80) cc_final: 0.6079 (t80) REVERT: A 290 TYR cc_start: 0.6687 (m-80) cc_final: 0.5702 (m-80) REVERT: A 314 MET cc_start: 0.7925 (mtt) cc_final: 0.7193 (tpt) REVERT: A 361 LYS cc_start: 0.8499 (mttt) cc_final: 0.7976 (tppt) REVERT: A 437 ASP cc_start: 0.8916 (t70) cc_final: 0.8496 (t0) REVERT: A 506 MET cc_start: 0.8769 (tpt) cc_final: 0.8476 (tpp) REVERT: A 517 ILE cc_start: 0.8443 (pt) cc_final: 0.8222 (tt) REVERT: A 526 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7354 (pttt) REVERT: A 603 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7687 (tmtt) REVERT: A 610 PHE cc_start: 0.7860 (m-80) cc_final: 0.7580 (m-10) REVERT: A 752 TRP cc_start: 0.8689 (t60) cc_final: 0.8486 (t60) REVERT: A 767 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 793 ARG cc_start: 0.8386 (ttp-110) cc_final: 0.7995 (ttm-80) REVERT: A 797 MET cc_start: 0.8358 (mtm) cc_final: 0.8113 (mtt) REVERT: A 824 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 856 ASP cc_start: 0.7595 (m-30) cc_final: 0.7128 (t0) REVERT: A 857 MET cc_start: 0.8534 (tpp) cc_final: 0.8240 (tpt) REVERT: B 238 LEU cc_start: 0.7180 (mt) cc_final: 0.6863 (mm) REVERT: B 242 PHE cc_start: 0.8381 (m-80) cc_final: 0.7819 (m-80) REVERT: B 279 TYR cc_start: 0.6537 (t80) cc_final: 0.6075 (t80) REVERT: B 290 TYR cc_start: 0.6689 (m-80) cc_final: 0.5719 (m-80) REVERT: B 314 MET cc_start: 0.7924 (mtt) cc_final: 0.7190 (tpt) REVERT: B 361 LYS cc_start: 0.8493 (mttt) cc_final: 0.7982 (tppt) REVERT: B 437 ASP cc_start: 0.8911 (t70) cc_final: 0.8336 (t0) REVERT: B 506 MET cc_start: 0.8772 (tpt) cc_final: 0.8469 (tpp) REVERT: B 517 ILE cc_start: 0.8442 (pt) cc_final: 0.8221 (tt) REVERT: B 526 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7359 (pttt) REVERT: B 603 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7659 (tmtt) REVERT: B 610 PHE cc_start: 0.7853 (m-80) cc_final: 0.7604 (m-10) REVERT: B 767 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 793 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7993 (ttm-80) REVERT: B 797 MET cc_start: 0.8354 (mtm) cc_final: 0.8115 (mtt) REVERT: B 824 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 856 ASP cc_start: 0.7598 (m-30) cc_final: 0.7128 (t0) REVERT: B 857 MET cc_start: 0.8540 (tpp) cc_final: 0.8245 (tpt) REVERT: B 1017 LEU cc_start: 0.8325 (mt) cc_final: 0.8100 (mt) REVERT: C 275 TRP cc_start: 0.4514 (p90) cc_final: 0.4294 (m-90) REVERT: C 286 SER cc_start: 0.7866 (m) cc_final: 0.7356 (t) REVERT: C 303 PHE cc_start: 0.7567 (m-10) cc_final: 0.7306 (m-80) REVERT: C 304 MET cc_start: 0.7135 (ppp) cc_final: 0.5861 (mtt) REVERT: C 306 PHE cc_start: 0.7838 (t80) cc_final: 0.7225 (t80) REVERT: C 314 MET cc_start: 0.3575 (mmt) cc_final: 0.3207 (mmt) REVERT: C 442 MET cc_start: 0.9077 (mmm) cc_final: 0.8873 (mmm) REVERT: C 513 MET cc_start: 0.7843 (mmm) cc_final: 0.7532 (mmt) REVERT: C 569 GLU cc_start: 0.8056 (tt0) cc_final: 0.7267 (pp20) REVERT: C 604 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8232 (tp30) REVERT: C 824 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8250 (tp30) REVERT: C 856 ASP cc_start: 0.8056 (m-30) cc_final: 0.7355 (t0) REVERT: C 857 MET cc_start: 0.8649 (tpp) cc_final: 0.8247 (tpt) REVERT: C 888 MET cc_start: 0.9120 (mtp) cc_final: 0.8800 (mtp) REVERT: C 955 ASP cc_start: 0.7185 (m-30) cc_final: 0.6533 (p0) REVERT: C 980 SER cc_start: 0.8921 (p) cc_final: 0.8695 (m) REVERT: C 983 SER cc_start: 0.9083 (m) cc_final: 0.8483 (p) REVERT: C 991 ILE cc_start: 0.8782 (mm) cc_final: 0.8568 (mm) REVERT: C 1029 ASN cc_start: 0.7791 (m110) cc_final: 0.7436 (m-40) REVERT: D 275 TRP cc_start: 0.4515 (p90) cc_final: 0.4308 (m-90) REVERT: D 286 SER cc_start: 0.7861 (m) cc_final: 0.7347 (t) REVERT: D 303 PHE cc_start: 0.7599 (m-10) cc_final: 0.7319 (m-80) REVERT: D 304 MET cc_start: 0.7124 (ppp) cc_final: 0.5849 (mtt) REVERT: D 306 PHE cc_start: 0.7839 (t80) cc_final: 0.7230 (t80) REVERT: D 314 MET cc_start: 0.3551 (mmt) cc_final: 0.3191 (mmt) REVERT: D 442 MET cc_start: 0.9079 (mmm) cc_final: 0.8875 (mmm) REVERT: D 513 MET cc_start: 0.7839 (mmm) cc_final: 0.7530 (mmt) REVERT: D 569 GLU cc_start: 0.8056 (tt0) cc_final: 0.7261 (pp20) REVERT: D 604 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8211 (tp30) REVERT: D 824 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8276 (tp30) REVERT: D 856 ASP cc_start: 0.8058 (m-30) cc_final: 0.7456 (t0) REVERT: D 857 MET cc_start: 0.8656 (tpp) cc_final: 0.8280 (tpt) REVERT: D 888 MET cc_start: 0.9126 (mtp) cc_final: 0.8809 (mtp) REVERT: D 955 ASP cc_start: 0.7178 (m-30) cc_final: 0.6536 (p0) REVERT: D 980 SER cc_start: 0.8918 (p) cc_final: 0.8693 (m) REVERT: D 983 SER cc_start: 0.9080 (m) cc_final: 0.8476 (p) REVERT: D 991 ILE cc_start: 0.8799 (mm) cc_final: 0.8585 (mm) REVERT: D 1029 ASN cc_start: 0.7825 (m110) cc_final: 0.7471 (m-40) outliers start: 11 outliers final: 2 residues processed: 542 average time/residue: 0.3599 time to fit residues: 294.0313 Evaluate side-chains 287 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 991 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 147 optimal weight: 0.0470 chunk 116 optimal weight: 0.9990 chunk 225 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 168 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 268 ASN A 384 ASN A 397 GLN A 451 HIS A 616 HIS A 803 ASN A 866 ASN A 867 ASN A1079 HIS B 237 ASN B 268 ASN B 384 ASN B 397 GLN B 451 HIS B 616 HIS B 803 ASN B 866 ASN B 867 ASN B1079 HIS C 372 ASN C 379 HIS C 427 ASN C 459 GLN C 534 ASN C 585 ASN C 811 HIS C 874 GLN C 942 ASN C 945 ASN D 372 ASN D 379 HIS D 427 ASN D 459 GLN D 534 ASN D 585 ASN D 811 HIS D 874 GLN D 942 ASN D 945 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23452 Z= 0.197 Angle : 0.611 9.605 31816 Z= 0.325 Chirality : 0.044 0.292 3660 Planarity : 0.005 0.045 4040 Dihedral : 6.299 80.320 3120 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 1.92 % Allowed : 7.30 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.14), residues: 2884 helix: -3.00 (0.12), residues: 1072 sheet: -1.54 (0.25), residues: 396 loop : -1.79 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 752 HIS 0.004 0.001 HIS B1079 PHE 0.029 0.002 PHE A1058 TYR 0.018 0.001 TYR C1073 ARG 0.004 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 350 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7315 (mt) cc_final: 0.7010 (mm) REVERT: A 242 PHE cc_start: 0.8346 (m-80) cc_final: 0.7619 (m-80) REVERT: A 279 TYR cc_start: 0.6265 (t80) cc_final: 0.5912 (t80) REVERT: A 290 TYR cc_start: 0.6749 (m-80) cc_final: 0.6051 (m-80) REVERT: A 314 MET cc_start: 0.7853 (mtt) cc_final: 0.7227 (tpt) REVERT: A 361 LYS cc_start: 0.8513 (mttt) cc_final: 0.8105 (tppt) REVERT: A 437 ASP cc_start: 0.8566 (t70) cc_final: 0.7206 (t0) REVERT: A 460 MET cc_start: 0.8217 (mmt) cc_final: 0.7620 (mmt) REVERT: A 506 MET cc_start: 0.8750 (tpt) cc_final: 0.8388 (tpp) REVERT: A 517 ILE cc_start: 0.8475 (pt) cc_final: 0.8222 (tt) REVERT: A 526 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7174 (pttt) REVERT: A 530 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7971 (mm-30) REVERT: A 749 MET cc_start: 0.8315 (mmt) cc_final: 0.7671 (mmt) REVERT: A 767 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8060 (mt-10) REVERT: A 802 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8063 (m) REVERT: A 824 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7182 (tp30) REVERT: A 856 ASP cc_start: 0.7571 (m-30) cc_final: 0.7298 (t0) REVERT: A 1067 MET cc_start: 0.7026 (ptp) cc_final: 0.6550 (ptp) REVERT: B 238 LEU cc_start: 0.7315 (mt) cc_final: 0.6999 (mm) REVERT: B 242 PHE cc_start: 0.8348 (m-80) cc_final: 0.7633 (m-80) REVERT: B 279 TYR cc_start: 0.6265 (t80) cc_final: 0.5916 (t80) REVERT: B 290 TYR cc_start: 0.6790 (m-80) cc_final: 0.6206 (m-80) REVERT: B 314 MET cc_start: 0.7854 (mtt) cc_final: 0.7228 (tpt) REVERT: B 361 LYS cc_start: 0.8518 (mttt) cc_final: 0.8039 (tppt) REVERT: B 437 ASP cc_start: 0.8744 (t70) cc_final: 0.8314 (t0) REVERT: B 506 MET cc_start: 0.8746 (tpt) cc_final: 0.8397 (tpp) REVERT: B 517 ILE cc_start: 0.8478 (pt) cc_final: 0.8221 (tt) REVERT: B 526 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7172 (pttt) REVERT: B 530 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7972 (mm-30) REVERT: B 749 MET cc_start: 0.8306 (mmt) cc_final: 0.7666 (mmt) REVERT: B 802 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8060 (m) REVERT: B 824 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7183 (tp30) REVERT: B 856 ASP cc_start: 0.7580 (m-30) cc_final: 0.7304 (t0) REVERT: B 1067 MET cc_start: 0.7033 (ptp) cc_final: 0.6559 (ptp) REVERT: C 282 MET cc_start: 0.6815 (tpt) cc_final: 0.6548 (mtp) REVERT: C 286 SER cc_start: 0.7910 (m) cc_final: 0.7351 (t) REVERT: C 303 PHE cc_start: 0.7742 (m-10) cc_final: 0.7447 (m-80) REVERT: C 304 MET cc_start: 0.6849 (ppp) cc_final: 0.5782 (mtt) REVERT: C 306 PHE cc_start: 0.7830 (t80) cc_final: 0.7319 (t80) REVERT: C 506 MET cc_start: 0.8526 (ttp) cc_final: 0.8306 (ttp) REVERT: C 604 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8282 (tp30) REVERT: C 752 TRP cc_start: 0.8089 (t60) cc_final: 0.7547 (t60) REVERT: C 824 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8521 (tp30) REVERT: C 856 ASP cc_start: 0.8029 (m-30) cc_final: 0.7493 (t0) REVERT: C 877 GLU cc_start: 0.7593 (mp0) cc_final: 0.7248 (mt-10) REVERT: C 955 ASP cc_start: 0.7048 (m-30) cc_final: 0.6503 (p0) REVERT: C 982 MET cc_start: 0.8640 (mmm) cc_final: 0.8334 (tpp) REVERT: C 1034 ARG cc_start: 0.1621 (pmm150) cc_final: 0.0405 (ptp90) REVERT: C 1038 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7548 (pp) REVERT: D 282 MET cc_start: 0.6789 (tpt) cc_final: 0.6518 (mtp) REVERT: D 286 SER cc_start: 0.7904 (m) cc_final: 0.7343 (t) REVERT: D 303 PHE cc_start: 0.7747 (m-10) cc_final: 0.7454 (m-80) REVERT: D 304 MET cc_start: 0.6831 (ppp) cc_final: 0.5795 (mtt) REVERT: D 306 PHE cc_start: 0.7834 (t80) cc_final: 0.7325 (t80) REVERT: D 506 MET cc_start: 0.8522 (ttp) cc_final: 0.8308 (ttp) REVERT: D 604 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8278 (tp30) REVERT: D 752 TRP cc_start: 0.8086 (t60) cc_final: 0.7536 (t60) REVERT: D 824 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8362 (tp30) REVERT: D 856 ASP cc_start: 0.8033 (m-30) cc_final: 0.7498 (t0) REVERT: D 877 GLU cc_start: 0.7586 (mp0) cc_final: 0.7289 (mt-10) REVERT: D 955 ASP cc_start: 0.7047 (m-30) cc_final: 0.6503 (p0) REVERT: D 982 MET cc_start: 0.8635 (mmm) cc_final: 0.8328 (tpp) REVERT: D 1034 ARG cc_start: 0.1617 (pmm150) cc_final: 0.0397 (ptp90) REVERT: D 1038 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7553 (pp) outliers start: 49 outliers final: 28 residues processed: 389 average time/residue: 0.3447 time to fit residues: 205.6352 Evaluate side-chains 306 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 1018 ARG Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 1018 ARG Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 262 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS A 751 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS B 751 HIS ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 HIS C1029 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 HIS D1029 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 23452 Z= 0.544 Angle : 0.777 7.888 31816 Z= 0.406 Chirality : 0.050 0.309 3660 Planarity : 0.005 0.046 4040 Dihedral : 6.610 74.735 3118 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.88 % Favored : 90.95 % Rotamer: Outliers : 2.94 % Allowed : 10.40 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.15), residues: 2884 helix: -2.49 (0.13), residues: 1094 sheet: -1.37 (0.26), residues: 398 loop : -1.71 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 246 HIS 0.010 0.002 HIS C 468 PHE 0.031 0.003 PHE D1070 TYR 0.023 0.002 TYR D1073 ARG 0.004 0.001 ARG B1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 266 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7329 (mt) cc_final: 0.7035 (mm) REVERT: A 242 PHE cc_start: 0.8464 (m-80) cc_final: 0.7861 (m-80) REVERT: A 279 TYR cc_start: 0.6626 (t80) cc_final: 0.6132 (t80) REVERT: A 290 TYR cc_start: 0.6782 (m-80) cc_final: 0.5912 (m-80) REVERT: A 314 MET cc_start: 0.7977 (mtt) cc_final: 0.7191 (tpt) REVERT: A 361 LYS cc_start: 0.8648 (mttt) cc_final: 0.8304 (tppt) REVERT: A 437 ASP cc_start: 0.8416 (t70) cc_final: 0.7037 (t0) REVERT: A 460 MET cc_start: 0.8308 (mmt) cc_final: 0.7639 (mmt) REVERT: A 506 MET cc_start: 0.8816 (tpt) cc_final: 0.8518 (tpp) REVERT: A 517 ILE cc_start: 0.8612 (pt) cc_final: 0.8347 (tt) REVERT: A 526 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7381 (pttt) REVERT: A 749 MET cc_start: 0.8247 (mmt) cc_final: 0.7730 (mmt) REVERT: A 802 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8313 (m) REVERT: A 1067 MET cc_start: 0.7225 (ptp) cc_final: 0.6577 (ptp) REVERT: B 238 LEU cc_start: 0.7301 (mt) cc_final: 0.7009 (mm) REVERT: B 242 PHE cc_start: 0.8461 (m-80) cc_final: 0.7858 (m-80) REVERT: B 279 TYR cc_start: 0.6617 (t80) cc_final: 0.6121 (t80) REVERT: B 290 TYR cc_start: 0.6798 (m-80) cc_final: 0.5956 (m-80) REVERT: B 314 MET cc_start: 0.7978 (mtt) cc_final: 0.7187 (tpt) REVERT: B 361 LYS cc_start: 0.8644 (mttt) cc_final: 0.8309 (tppt) REVERT: B 437 ASP cc_start: 0.8419 (t70) cc_final: 0.7891 (t0) REVERT: B 517 ILE cc_start: 0.8611 (pt) cc_final: 0.8344 (tt) REVERT: B 526 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7383 (pttt) REVERT: B 749 MET cc_start: 0.8242 (mmt) cc_final: 0.7730 (mmt) REVERT: B 802 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8311 (m) REVERT: B 1067 MET cc_start: 0.7273 (ptp) cc_final: 0.6629 (ptp) REVERT: C 285 MET cc_start: 0.6718 (ptt) cc_final: 0.6249 (ptt) REVERT: C 286 SER cc_start: 0.7568 (m) cc_final: 0.6942 (t) REVERT: C 303 PHE cc_start: 0.7930 (m-10) cc_final: 0.7645 (m-80) REVERT: C 304 MET cc_start: 0.6914 (ppp) cc_final: 0.5956 (mtt) REVERT: C 306 PHE cc_start: 0.7892 (t80) cc_final: 0.7385 (t80) REVERT: C 752 TRP cc_start: 0.8338 (t60) cc_final: 0.8031 (t60) REVERT: C 789 LEU cc_start: 0.8097 (mt) cc_final: 0.7836 (mt) REVERT: C 824 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8178 (tp30) REVERT: C 856 ASP cc_start: 0.7837 (m-30) cc_final: 0.7415 (t0) REVERT: C 955 ASP cc_start: 0.7165 (m-30) cc_final: 0.6730 (p0) REVERT: D 285 MET cc_start: 0.6737 (ptt) cc_final: 0.6268 (ptt) REVERT: D 286 SER cc_start: 0.7553 (m) cc_final: 0.6923 (t) REVERT: D 303 PHE cc_start: 0.7932 (m-10) cc_final: 0.7651 (m-80) REVERT: D 304 MET cc_start: 0.6910 (ppp) cc_final: 0.5947 (mtt) REVERT: D 306 PHE cc_start: 0.7893 (t80) cc_final: 0.7389 (t80) REVERT: D 752 TRP cc_start: 0.8329 (t60) cc_final: 0.8086 (t60) REVERT: D 824 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8436 (tp30) REVERT: D 856 ASP cc_start: 0.7836 (m-30) cc_final: 0.7415 (t0) REVERT: D 955 ASP cc_start: 0.7158 (m-30) cc_final: 0.6730 (p0) outliers start: 75 outliers final: 57 residues processed: 321 average time/residue: 0.3129 time to fit residues: 161.7857 Evaluate side-chains 303 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23452 Z= 0.174 Angle : 0.556 8.990 31816 Z= 0.291 Chirality : 0.043 0.228 3660 Planarity : 0.004 0.041 4040 Dihedral : 5.715 67.311 3116 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 2.47 % Allowed : 11.81 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.15), residues: 2884 helix: -2.02 (0.14), residues: 1080 sheet: -0.97 (0.27), residues: 396 loop : -1.39 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 752 HIS 0.003 0.001 HIS A1079 PHE 0.021 0.001 PHE D1070 TYR 0.011 0.001 TYR A 962 ARG 0.003 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 290 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7113 (mt) cc_final: 0.6815 (mm) REVERT: A 242 PHE cc_start: 0.8447 (m-80) cc_final: 0.8155 (m-80) REVERT: A 279 TYR cc_start: 0.6599 (t80) cc_final: 0.6174 (t80) REVERT: A 282 MET cc_start: 0.6594 (mmt) cc_final: 0.6238 (mmt) REVERT: A 290 TYR cc_start: 0.6889 (m-80) cc_final: 0.6012 (m-80) REVERT: A 304 MET cc_start: 0.8576 (ptt) cc_final: 0.7869 (mmt) REVERT: A 314 MET cc_start: 0.8067 (mtt) cc_final: 0.7259 (tpt) REVERT: A 361 LYS cc_start: 0.8636 (mttt) cc_final: 0.8307 (tppt) REVERT: A 437 ASP cc_start: 0.8361 (t70) cc_final: 0.7835 (t0) REVERT: A 506 MET cc_start: 0.8786 (tpt) cc_final: 0.8405 (ttm) REVERT: A 517 ILE cc_start: 0.8546 (pt) cc_final: 0.8299 (tt) REVERT: A 526 LYS cc_start: 0.8090 (ttpt) cc_final: 0.6952 (pttt) REVERT: A 530 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8070 (mm-30) REVERT: A 569 GLU cc_start: 0.7391 (tp30) cc_final: 0.7139 (tp30) REVERT: A 587 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7927 (tt) REVERT: A 749 MET cc_start: 0.8303 (mmt) cc_final: 0.7783 (mmt) REVERT: A 802 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8144 (m) REVERT: A 857 MET cc_start: 0.8410 (mmm) cc_final: 0.8156 (mmm) REVERT: A 1008 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8029 (tm-30) REVERT: A 1067 MET cc_start: 0.7178 (ptp) cc_final: 0.6740 (ptp) REVERT: B 238 LEU cc_start: 0.7115 (mt) cc_final: 0.6813 (mm) REVERT: B 242 PHE cc_start: 0.8450 (m-80) cc_final: 0.8156 (m-80) REVERT: B 279 TYR cc_start: 0.6536 (t80) cc_final: 0.6108 (t80) REVERT: B 282 MET cc_start: 0.6592 (mmt) cc_final: 0.6235 (mmt) REVERT: B 290 TYR cc_start: 0.6886 (m-80) cc_final: 0.5979 (m-80) REVERT: B 304 MET cc_start: 0.8616 (ptt) cc_final: 0.7834 (mmt) REVERT: B 314 MET cc_start: 0.8068 (mtt) cc_final: 0.7256 (tpt) REVERT: B 361 LYS cc_start: 0.8629 (mttt) cc_final: 0.8311 (tppt) REVERT: B 437 ASP cc_start: 0.8416 (t70) cc_final: 0.7853 (t0) REVERT: B 506 MET cc_start: 0.8797 (tpp) cc_final: 0.8465 (tpp) REVERT: B 517 ILE cc_start: 0.8545 (pt) cc_final: 0.8287 (tt) REVERT: B 526 LYS cc_start: 0.8090 (ttpt) cc_final: 0.6956 (pttt) REVERT: B 530 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8072 (mm-30) REVERT: B 569 GLU cc_start: 0.7384 (tp30) cc_final: 0.7131 (tp30) REVERT: B 587 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 749 MET cc_start: 0.8298 (mmt) cc_final: 0.7794 (mmt) REVERT: B 802 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8140 (m) REVERT: B 857 MET cc_start: 0.8418 (mmm) cc_final: 0.8168 (mmm) REVERT: B 875 ASP cc_start: 0.7617 (m-30) cc_final: 0.7393 (m-30) REVERT: B 1008 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7910 (tm-30) REVERT: B 1067 MET cc_start: 0.7173 (ptp) cc_final: 0.6739 (ptp) REVERT: C 286 SER cc_start: 0.7571 (m) cc_final: 0.7115 (t) REVERT: C 303 PHE cc_start: 0.7893 (m-10) cc_final: 0.7618 (m-80) REVERT: C 304 MET cc_start: 0.6971 (ppp) cc_final: 0.6104 (mtt) REVERT: C 306 PHE cc_start: 0.7857 (t80) cc_final: 0.7348 (t80) REVERT: C 824 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8200 (tp30) REVERT: C 955 ASP cc_start: 0.7171 (m-30) cc_final: 0.6651 (p0) REVERT: C 1034 ARG cc_start: 0.1926 (pmm150) cc_final: 0.0945 (ptp90) REVERT: C 1038 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7639 (pp) REVERT: D 286 SER cc_start: 0.7560 (m) cc_final: 0.7108 (t) REVERT: D 303 PHE cc_start: 0.7897 (m-10) cc_final: 0.7621 (m-80) REVERT: D 304 MET cc_start: 0.6967 (ppp) cc_final: 0.6102 (mtt) REVERT: D 306 PHE cc_start: 0.7855 (t80) cc_final: 0.7350 (t80) REVERT: D 609 PHE cc_start: 0.7745 (t80) cc_final: 0.7540 (t80) REVERT: D 824 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8370 (tp30) REVERT: D 955 ASP cc_start: 0.7170 (m-30) cc_final: 0.6653 (p0) REVERT: D 1034 ARG cc_start: 0.1912 (pmm150) cc_final: 0.0944 (ptp90) REVERT: D 1038 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7631 (pp) outliers start: 63 outliers final: 40 residues processed: 332 average time/residue: 0.3358 time to fit residues: 174.4334 Evaluate side-chains 304 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN A 942 ASN ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 GLN B 942 ASN C 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23452 Z= 0.287 Angle : 0.599 7.517 31816 Z= 0.309 Chirality : 0.045 0.302 3660 Planarity : 0.004 0.039 4040 Dihedral : 5.654 66.963 3116 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.14 % Favored : 92.79 % Rotamer: Outliers : 3.10 % Allowed : 12.68 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2884 helix: -1.76 (0.14), residues: 1094 sheet: -0.92 (0.27), residues: 392 loop : -1.35 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 246 HIS 0.005 0.001 HIS C 468 PHE 0.021 0.002 PHE A 558 TYR 0.013 0.001 TYR C1073 ARG 0.006 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 275 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.6632 (t80) cc_final: 0.6177 (t80) REVERT: A 290 TYR cc_start: 0.6895 (m-80) cc_final: 0.5933 (m-80) REVERT: A 304 MET cc_start: 0.8597 (ptt) cc_final: 0.7815 (mmt) REVERT: A 314 MET cc_start: 0.8017 (mtt) cc_final: 0.7661 (ppp) REVERT: A 361 LYS cc_start: 0.8653 (mttt) cc_final: 0.8339 (tppt) REVERT: A 437 ASP cc_start: 0.8350 (t70) cc_final: 0.7744 (t0) REVERT: A 506 MET cc_start: 0.8876 (tpt) cc_final: 0.8513 (tpt) REVERT: A 517 ILE cc_start: 0.8469 (pt) cc_final: 0.8194 (tt) REVERT: A 526 LYS cc_start: 0.8003 (ttpt) cc_final: 0.6910 (pttt) REVERT: A 530 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8083 (mm-30) REVERT: A 569 GLU cc_start: 0.7435 (tp30) cc_final: 0.7150 (tp30) REVERT: A 587 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 749 MET cc_start: 0.8284 (mmt) cc_final: 0.7784 (mmt) REVERT: A 784 ASP cc_start: 0.6754 (p0) cc_final: 0.6486 (p0) REVERT: A 802 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8166 (m) REVERT: A 1067 MET cc_start: 0.7178 (ptp) cc_final: 0.6667 (ptp) REVERT: B 242 PHE cc_start: 0.8242 (m-80) cc_final: 0.7745 (m-10) REVERT: B 279 TYR cc_start: 0.6628 (t80) cc_final: 0.6180 (t80) REVERT: B 290 TYR cc_start: 0.6964 (m-80) cc_final: 0.6055 (m-80) REVERT: B 304 MET cc_start: 0.8636 (ptt) cc_final: 0.7831 (mmt) REVERT: B 314 MET cc_start: 0.8022 (mtt) cc_final: 0.7158 (tpp) REVERT: B 361 LYS cc_start: 0.8648 (mttt) cc_final: 0.8337 (tppt) REVERT: B 437 ASP cc_start: 0.8458 (t70) cc_final: 0.8024 (t0) REVERT: B 506 MET cc_start: 0.8904 (tpp) cc_final: 0.8544 (tpp) REVERT: B 517 ILE cc_start: 0.8464 (pt) cc_final: 0.8190 (tt) REVERT: B 526 LYS cc_start: 0.8003 (ttpt) cc_final: 0.6908 (pttt) REVERT: B 530 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8090 (mm-30) REVERT: B 569 GLU cc_start: 0.7429 (tp30) cc_final: 0.7141 (tp30) REVERT: B 587 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 749 MET cc_start: 0.8277 (mmt) cc_final: 0.7779 (mmt) REVERT: B 784 ASP cc_start: 0.6763 (p0) cc_final: 0.6497 (p0) REVERT: B 802 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 1067 MET cc_start: 0.7179 (ptp) cc_final: 0.6668 (ptp) REVERT: C 286 SER cc_start: 0.7535 (m) cc_final: 0.7056 (t) REVERT: C 304 MET cc_start: 0.6968 (ppp) cc_final: 0.6063 (mtt) REVERT: C 306 PHE cc_start: 0.7878 (t80) cc_final: 0.7371 (t80) REVERT: C 506 MET cc_start: 0.8509 (ttp) cc_final: 0.8268 (ttm) REVERT: C 824 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8030 (tp30) REVERT: C 955 ASP cc_start: 0.7224 (m-30) cc_final: 0.6709 (p0) REVERT: C 1034 ARG cc_start: 0.2014 (pmm150) cc_final: 0.0896 (ptp90) REVERT: C 1038 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7651 (pp) REVERT: D 286 SER cc_start: 0.7524 (m) cc_final: 0.7045 (t) REVERT: D 304 MET cc_start: 0.6962 (ppp) cc_final: 0.6056 (mtt) REVERT: D 306 PHE cc_start: 0.7883 (t80) cc_final: 0.7362 (t80) REVERT: D 506 MET cc_start: 0.8507 (ttp) cc_final: 0.8268 (ttm) REVERT: D 824 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8387 (tp30) REVERT: D 955 ASP cc_start: 0.7220 (m-30) cc_final: 0.6709 (p0) REVERT: D 1034 ARG cc_start: 0.2072 (pmm150) cc_final: 0.0961 (ptp90) REVERT: D 1038 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7662 (pp) outliers start: 79 outliers final: 59 residues processed: 328 average time/residue: 0.3187 time to fit residues: 167.4684 Evaluate side-chains 323 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 258 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23452 Z= 0.200 Angle : 0.552 7.940 31816 Z= 0.285 Chirality : 0.044 0.314 3660 Planarity : 0.003 0.037 4040 Dihedral : 5.375 62.860 3116 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 3.10 % Allowed : 12.99 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2884 helix: -1.44 (0.15), residues: 1096 sheet: -0.88 (0.27), residues: 388 loop : -1.15 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 752 HIS 0.003 0.001 HIS C 468 PHE 0.021 0.001 PHE D1070 TYR 0.011 0.001 TYR C1065 ARG 0.004 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 278 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8113 (m-80) cc_final: 0.7759 (m-80) REVERT: A 279 TYR cc_start: 0.6644 (t80) cc_final: 0.6232 (t80) REVERT: A 290 TYR cc_start: 0.7000 (m-80) cc_final: 0.6125 (m-80) REVERT: A 304 MET cc_start: 0.8601 (ptt) cc_final: 0.7764 (mmt) REVERT: A 314 MET cc_start: 0.8170 (mtt) cc_final: 0.7253 (tpp) REVERT: A 361 LYS cc_start: 0.8653 (mttt) cc_final: 0.8347 (tppt) REVERT: A 437 ASP cc_start: 0.8381 (t70) cc_final: 0.7832 (t0) REVERT: A 506 MET cc_start: 0.8836 (tpt) cc_final: 0.8511 (ttm) REVERT: A 517 ILE cc_start: 0.8476 (pt) cc_final: 0.8211 (tt) REVERT: A 526 LYS cc_start: 0.7939 (ttpt) cc_final: 0.6855 (pttt) REVERT: A 530 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8085 (mm-30) REVERT: A 569 GLU cc_start: 0.7439 (tp30) cc_final: 0.6932 (tp30) REVERT: A 587 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7977 (tt) REVERT: A 802 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (m) REVERT: A 1067 MET cc_start: 0.7132 (ptp) cc_final: 0.6742 (ptp) REVERT: B 279 TYR cc_start: 0.6646 (t80) cc_final: 0.6234 (t80) REVERT: B 290 TYR cc_start: 0.6944 (m-80) cc_final: 0.6017 (m-80) REVERT: B 304 MET cc_start: 0.8605 (ptt) cc_final: 0.7764 (mmt) REVERT: B 314 MET cc_start: 0.8169 (mtt) cc_final: 0.7808 (ppp) REVERT: B 361 LYS cc_start: 0.8635 (mttt) cc_final: 0.8340 (tppt) REVERT: B 437 ASP cc_start: 0.8591 (t70) cc_final: 0.8231 (t0) REVERT: B 506 MET cc_start: 0.8862 (tpp) cc_final: 0.8375 (tpp) REVERT: B 517 ILE cc_start: 0.8472 (pt) cc_final: 0.8194 (tt) REVERT: B 526 LYS cc_start: 0.7941 (ttpt) cc_final: 0.6856 (pttt) REVERT: B 530 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8114 (mm-30) REVERT: B 569 GLU cc_start: 0.7433 (tp30) cc_final: 0.6928 (tp30) REVERT: B 587 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (tt) REVERT: B 802 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8125 (m) REVERT: B 1067 MET cc_start: 0.7132 (ptp) cc_final: 0.6743 (ptp) REVERT: C 286 SER cc_start: 0.7528 (m) cc_final: 0.7110 (t) REVERT: C 304 MET cc_start: 0.6825 (ppp) cc_final: 0.6080 (mtt) REVERT: C 306 PHE cc_start: 0.7925 (t80) cc_final: 0.7449 (t80) REVERT: C 479 GLU cc_start: 0.8092 (tm-30) cc_final: 0.6933 (tm-30) REVERT: C 824 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8144 (tp30) REVERT: C 955 ASP cc_start: 0.7216 (m-30) cc_final: 0.6675 (p0) REVERT: C 960 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: C 983 SER cc_start: 0.8946 (m) cc_final: 0.8592 (p) REVERT: C 1034 ARG cc_start: 0.1859 (pmm150) cc_final: 0.1595 (pmm150) REVERT: C 1038 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7665 (pp) REVERT: D 286 SER cc_start: 0.7515 (m) cc_final: 0.7080 (t) REVERT: D 304 MET cc_start: 0.6818 (ppp) cc_final: 0.6074 (mtt) REVERT: D 306 PHE cc_start: 0.7928 (t80) cc_final: 0.7453 (t80) REVERT: D 479 GLU cc_start: 0.8077 (tm-30) cc_final: 0.6965 (tm-30) REVERT: D 824 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8382 (tp30) REVERT: D 955 ASP cc_start: 0.7213 (m-30) cc_final: 0.6676 (p0) REVERT: D 960 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: D 983 SER cc_start: 0.8941 (m) cc_final: 0.8582 (p) REVERT: D 1034 ARG cc_start: 0.1846 (pmm150) cc_final: 0.1606 (pmm150) REVERT: D 1038 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7664 (pp) outliers start: 79 outliers final: 55 residues processed: 329 average time/residue: 0.3342 time to fit residues: 172.5417 Evaluate side-chains 323 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 260 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 0.2980 chunk 157 optimal weight: 0.1980 chunk 234 optimal weight: 0.0070 chunk 155 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 794 ASN A 803 ASN B 372 ASN B 803 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23452 Z= 0.143 Angle : 0.525 8.539 31816 Z= 0.270 Chirality : 0.043 0.289 3660 Planarity : 0.003 0.036 4040 Dihedral : 5.014 56.132 3116 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 2.98 % Allowed : 13.30 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2884 helix: -1.18 (0.15), residues: 1126 sheet: -0.79 (0.28), residues: 388 loop : -1.10 (0.18), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 752 HIS 0.003 0.000 HIS B 365 PHE 0.023 0.001 PHE D1070 TYR 0.012 0.001 TYR B 962 ARG 0.005 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 299 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.6608 (t80) cc_final: 0.6233 (t80) REVERT: A 290 TYR cc_start: 0.7054 (m-80) cc_final: 0.6178 (m-80) REVERT: A 304 MET cc_start: 0.8599 (ptt) cc_final: 0.7754 (mmt) REVERT: A 361 LYS cc_start: 0.8640 (mttt) cc_final: 0.8329 (tppt) REVERT: A 372 ASN cc_start: 0.7211 (t0) cc_final: 0.6686 (t0) REVERT: A 437 ASP cc_start: 0.8397 (t70) cc_final: 0.7905 (t0) REVERT: A 460 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7885 (mmm) REVERT: A 517 ILE cc_start: 0.8453 (pt) cc_final: 0.8172 (tt) REVERT: A 526 LYS cc_start: 0.7878 (ttpt) cc_final: 0.6745 (pttt) REVERT: A 530 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8002 (mm-30) REVERT: A 569 GLU cc_start: 0.7512 (tp30) cc_final: 0.7040 (tp30) REVERT: A 587 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7949 (tt) REVERT: A 749 MET cc_start: 0.8229 (mmt) cc_final: 0.7765 (mmt) REVERT: A 802 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7948 (m) REVERT: A 1067 MET cc_start: 0.6974 (ptp) cc_final: 0.6713 (ptp) REVERT: B 242 PHE cc_start: 0.8089 (m-80) cc_final: 0.7730 (m-80) REVERT: B 279 TYR cc_start: 0.6609 (t80) cc_final: 0.6234 (t80) REVERT: B 290 TYR cc_start: 0.7042 (m-80) cc_final: 0.6181 (m-80) REVERT: B 304 MET cc_start: 0.8590 (ptt) cc_final: 0.7742 (mmt) REVERT: B 314 MET cc_start: 0.8233 (mtt) cc_final: 0.7264 (tpp) REVERT: B 361 LYS cc_start: 0.8589 (mttt) cc_final: 0.8299 (tppt) REVERT: B 372 ASN cc_start: 0.7203 (t0) cc_final: 0.6684 (t0) REVERT: B 437 ASP cc_start: 0.8606 (t70) cc_final: 0.8320 (t0) REVERT: B 517 ILE cc_start: 0.8469 (pt) cc_final: 0.8187 (tt) REVERT: B 526 LYS cc_start: 0.7792 (ttpt) cc_final: 0.6628 (pttt) REVERT: B 530 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7888 (mm-30) REVERT: B 569 GLU cc_start: 0.7508 (tp30) cc_final: 0.7044 (tp30) REVERT: B 587 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7950 (tt) REVERT: B 749 MET cc_start: 0.8215 (mmt) cc_final: 0.7751 (mmt) REVERT: B 802 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7945 (m) REVERT: B 1067 MET cc_start: 0.6971 (ptp) cc_final: 0.6681 (ptp) REVERT: C 286 SER cc_start: 0.7457 (m) cc_final: 0.7054 (t) REVERT: C 303 PHE cc_start: 0.7902 (m-10) cc_final: 0.7613 (m-80) REVERT: C 304 MET cc_start: 0.6764 (ppp) cc_final: 0.6083 (mtt) REVERT: C 378 LEU cc_start: 0.8388 (tp) cc_final: 0.8175 (tp) REVERT: C 479 GLU cc_start: 0.8050 (tm-30) cc_final: 0.6886 (tm-30) REVERT: C 530 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7684 (mm-30) REVERT: C 789 LEU cc_start: 0.8027 (tp) cc_final: 0.7493 (tp) REVERT: C 824 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7971 (tp30) REVERT: C 955 ASP cc_start: 0.7311 (m-30) cc_final: 0.6669 (p0) REVERT: C 983 SER cc_start: 0.8907 (m) cc_final: 0.8570 (p) REVERT: C 1038 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7558 (pp) REVERT: D 286 SER cc_start: 0.7453 (m) cc_final: 0.7045 (t) REVERT: D 303 PHE cc_start: 0.7902 (m-10) cc_final: 0.7614 (m-80) REVERT: D 304 MET cc_start: 0.6791 (ppp) cc_final: 0.6126 (mtt) REVERT: D 378 LEU cc_start: 0.8384 (tp) cc_final: 0.8170 (tp) REVERT: D 479 GLU cc_start: 0.8047 (tm-30) cc_final: 0.6881 (tm-30) REVERT: D 530 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7690 (mm-30) REVERT: D 824 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8315 (tp30) REVERT: D 955 ASP cc_start: 0.7308 (m-30) cc_final: 0.6665 (p0) REVERT: D 983 SER cc_start: 0.8899 (m) cc_final: 0.8560 (p) REVERT: D 1038 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7563 (pp) outliers start: 76 outliers final: 55 residues processed: 349 average time/residue: 0.3378 time to fit residues: 185.1534 Evaluate side-chains 341 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 279 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1018 ARG Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23452 Z= 0.331 Angle : 0.605 9.020 31816 Z= 0.309 Chirality : 0.046 0.317 3660 Planarity : 0.004 0.046 4040 Dihedral : 5.294 59.983 3116 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.82 % Rotamer: Outliers : 3.34 % Allowed : 12.91 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2884 helix: -1.17 (0.15), residues: 1100 sheet: -0.93 (0.27), residues: 390 loop : -0.99 (0.18), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 752 HIS 0.005 0.001 HIS C 829 PHE 0.029 0.002 PHE D1070 TYR 0.012 0.001 TYR D1073 ARG 0.006 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 269 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7908 (m-80) cc_final: 0.7540 (m-80) REVERT: A 279 TYR cc_start: 0.6615 (t80) cc_final: 0.6297 (t80) REVERT: A 290 TYR cc_start: 0.7232 (m-80) cc_final: 0.6370 (m-80) REVERT: A 304 MET cc_start: 0.8624 (ptt) cc_final: 0.7791 (mmt) REVERT: A 314 MET cc_start: 0.8168 (mtt) cc_final: 0.7168 (tpp) REVERT: A 361 LYS cc_start: 0.8669 (mttt) cc_final: 0.8387 (tppt) REVERT: A 372 ASN cc_start: 0.7321 (t0) cc_final: 0.6952 (t0) REVERT: A 437 ASP cc_start: 0.8347 (t70) cc_final: 0.7705 (t0) REVERT: A 459 GLN cc_start: 0.8279 (mt0) cc_final: 0.8042 (mm-40) REVERT: A 460 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8025 (mmm) REVERT: A 517 ILE cc_start: 0.8461 (pt) cc_final: 0.8226 (tt) REVERT: A 526 LYS cc_start: 0.8004 (ttpt) cc_final: 0.6858 (pttt) REVERT: A 530 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8134 (mm-30) REVERT: A 587 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8006 (tt) REVERT: A 802 SER cc_start: 0.8606 (t) cc_final: 0.8312 (m) REVERT: A 1018 ARG cc_start: 0.6866 (mpt-90) cc_final: 0.6593 (mpt-90) REVERT: A 1067 MET cc_start: 0.7118 (ptp) cc_final: 0.6750 (ptp) REVERT: B 279 TYR cc_start: 0.6617 (t80) cc_final: 0.6300 (t80) REVERT: B 290 TYR cc_start: 0.7254 (m-80) cc_final: 0.6406 (m-80) REVERT: B 304 MET cc_start: 0.8597 (ptt) cc_final: 0.7745 (mmt) REVERT: B 361 LYS cc_start: 0.8640 (mttt) cc_final: 0.8362 (tppt) REVERT: B 372 ASN cc_start: 0.7314 (t0) cc_final: 0.6950 (t0) REVERT: B 437 ASP cc_start: 0.8536 (t70) cc_final: 0.8132 (t0) REVERT: B 459 GLN cc_start: 0.8289 (mt0) cc_final: 0.8073 (mm-40) REVERT: B 517 ILE cc_start: 0.8453 (pt) cc_final: 0.8212 (tt) REVERT: B 526 LYS cc_start: 0.7911 (ttpt) cc_final: 0.6723 (pttt) REVERT: B 530 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7903 (mm-30) REVERT: B 587 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8007 (tt) REVERT: B 802 SER cc_start: 0.8607 (t) cc_final: 0.8307 (m) REVERT: B 1018 ARG cc_start: 0.6923 (mpt-90) cc_final: 0.6637 (mpt-90) REVERT: B 1067 MET cc_start: 0.7107 (ptp) cc_final: 0.6827 (ptp) REVERT: C 286 SER cc_start: 0.7544 (m) cc_final: 0.7146 (t) REVERT: C 303 PHE cc_start: 0.7934 (m-10) cc_final: 0.7627 (m-80) REVERT: C 304 MET cc_start: 0.6825 (ppp) cc_final: 0.6120 (mtt) REVERT: C 378 LEU cc_start: 0.8475 (tp) cc_final: 0.8263 (tp) REVERT: C 824 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8115 (tp30) REVERT: C 955 ASP cc_start: 0.7183 (m-30) cc_final: 0.6678 (p0) REVERT: C 960 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: C 1038 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7643 (pp) REVERT: C 1090 TYR cc_start: 0.8456 (p90) cc_final: 0.7965 (p90) REVERT: D 286 SER cc_start: 0.7539 (m) cc_final: 0.7138 (t) REVERT: D 303 PHE cc_start: 0.7933 (m-10) cc_final: 0.7628 (m-80) REVERT: D 304 MET cc_start: 0.6817 (ppp) cc_final: 0.6115 (mtt) REVERT: D 752 TRP cc_start: 0.8294 (t60) cc_final: 0.7903 (t60) REVERT: D 824 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8274 (tp30) REVERT: D 955 ASP cc_start: 0.7184 (m-30) cc_final: 0.6674 (p0) REVERT: D 960 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: D 1038 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7698 (pp) REVERT: D 1090 TYR cc_start: 0.8458 (p90) cc_final: 0.7971 (p90) outliers start: 85 outliers final: 64 residues processed: 332 average time/residue: 0.3285 time to fit residues: 172.7093 Evaluate side-chains 319 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 248 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 958 ASP Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1018 ARG Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 958 ASP Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23452 Z= 0.205 Angle : 0.556 9.285 31816 Z= 0.284 Chirality : 0.044 0.318 3660 Planarity : 0.003 0.036 4040 Dihedral : 5.073 47.597 3116 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 2.94 % Allowed : 14.01 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2884 helix: -1.08 (0.15), residues: 1112 sheet: -0.97 (0.28), residues: 380 loop : -0.94 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 752 HIS 0.004 0.001 HIS C 468 PHE 0.029 0.001 PHE D1070 TYR 0.013 0.001 TYR C 274 ARG 0.005 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 259 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8106 (m-80) cc_final: 0.7704 (m-80) REVERT: A 279 TYR cc_start: 0.6575 (t80) cc_final: 0.6274 (t80) REVERT: A 290 TYR cc_start: 0.7264 (m-80) cc_final: 0.6428 (m-80) REVERT: A 304 MET cc_start: 0.8616 (ptt) cc_final: 0.7786 (mmt) REVERT: A 314 MET cc_start: 0.8165 (mtt) cc_final: 0.7163 (tpp) REVERT: A 361 LYS cc_start: 0.8657 (mttt) cc_final: 0.8398 (tppt) REVERT: A 437 ASP cc_start: 0.8395 (t70) cc_final: 0.7778 (t0) REVERT: A 460 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7992 (mmm) REVERT: A 506 MET cc_start: 0.8914 (tpp) cc_final: 0.8236 (ttm) REVERT: A 517 ILE cc_start: 0.8441 (pt) cc_final: 0.8186 (tt) REVERT: A 526 LYS cc_start: 0.7876 (ttpt) cc_final: 0.6773 (pttt) REVERT: A 530 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8115 (mm-30) REVERT: A 587 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7995 (tt) REVERT: A 802 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8341 (m) REVERT: A 1018 ARG cc_start: 0.6935 (mpt-90) cc_final: 0.6643 (mpt-90) REVERT: A 1067 MET cc_start: 0.7054 (ptp) cc_final: 0.6738 (ptp) REVERT: B 242 PHE cc_start: 0.8069 (m-80) cc_final: 0.7707 (m-80) REVERT: B 279 TYR cc_start: 0.6567 (t80) cc_final: 0.6271 (t80) REVERT: B 290 TYR cc_start: 0.7269 (m-80) cc_final: 0.6448 (m-80) REVERT: B 304 MET cc_start: 0.8613 (ptt) cc_final: 0.7735 (mmt) REVERT: B 314 MET cc_start: 0.8163 (mtt) cc_final: 0.7194 (tpp) REVERT: B 361 LYS cc_start: 0.8629 (mttt) cc_final: 0.8367 (tppt) REVERT: B 437 ASP cc_start: 0.8586 (t70) cc_final: 0.8222 (t0) REVERT: B 517 ILE cc_start: 0.8433 (pt) cc_final: 0.8167 (tt) REVERT: B 526 LYS cc_start: 0.7741 (ttpt) cc_final: 0.6574 (pttt) REVERT: B 530 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7867 (mm-30) REVERT: B 587 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7996 (tt) REVERT: B 802 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8340 (m) REVERT: B 1018 ARG cc_start: 0.6898 (mpt-90) cc_final: 0.6622 (mpt-90) REVERT: B 1067 MET cc_start: 0.7072 (ptp) cc_final: 0.6811 (ptp) REVERT: C 286 SER cc_start: 0.7503 (m) cc_final: 0.7110 (t) REVERT: C 303 PHE cc_start: 0.7897 (m-10) cc_final: 0.7588 (m-80) REVERT: C 304 MET cc_start: 0.6838 (ppp) cc_final: 0.6217 (mtt) REVERT: C 378 LEU cc_start: 0.8464 (tp) cc_final: 0.8256 (tp) REVERT: C 442 MET cc_start: 0.8768 (mmm) cc_final: 0.8550 (mmp) REVERT: C 479 GLU cc_start: 0.8020 (tm-30) cc_final: 0.6802 (tm-30) REVERT: C 752 TRP cc_start: 0.8246 (t60) cc_final: 0.7915 (t60) REVERT: C 824 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8141 (tp30) REVERT: C 955 ASP cc_start: 0.7413 (m-30) cc_final: 0.6760 (p0) REVERT: C 960 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 983 SER cc_start: 0.8958 (m) cc_final: 0.8483 (p) REVERT: C 1038 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7658 (pp) REVERT: C 1090 TYR cc_start: 0.8439 (p90) cc_final: 0.7948 (p90) REVERT: D 286 SER cc_start: 0.7502 (m) cc_final: 0.7104 (t) REVERT: D 303 PHE cc_start: 0.7921 (m-10) cc_final: 0.7608 (m-80) REVERT: D 304 MET cc_start: 0.6832 (ppp) cc_final: 0.6212 (mtt) REVERT: D 378 LEU cc_start: 0.8461 (tp) cc_final: 0.8251 (tp) REVERT: D 479 GLU cc_start: 0.8022 (tm-30) cc_final: 0.6804 (tm-30) REVERT: D 752 TRP cc_start: 0.8230 (t60) cc_final: 0.7830 (t60) REVERT: D 955 ASP cc_start: 0.7413 (m-30) cc_final: 0.6757 (p0) REVERT: D 960 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: D 983 SER cc_start: 0.8940 (m) cc_final: 0.8464 (p) REVERT: D 1038 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7664 (pp) REVERT: D 1090 TYR cc_start: 0.8440 (p90) cc_final: 0.7959 (p90) outliers start: 75 outliers final: 60 residues processed: 314 average time/residue: 0.3171 time to fit residues: 158.4562 Evaluate side-chains 317 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 248 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1038 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 10.0000 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23452 Z= 0.179 Angle : 0.549 9.315 31816 Z= 0.279 Chirality : 0.044 0.316 3660 Planarity : 0.003 0.037 4040 Dihedral : 4.887 42.594 3116 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 2.63 % Allowed : 14.60 % Favored : 82.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.16), residues: 2884 helix: -0.92 (0.15), residues: 1112 sheet: -1.00 (0.28), residues: 360 loop : -0.83 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 752 HIS 0.003 0.001 HIS C 468 PHE 0.027 0.001 PHE D1070 TYR 0.012 0.001 TYR B1090 ARG 0.005 0.000 ARG B 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 258 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8091 (m-80) cc_final: 0.7701 (m-80) REVERT: A 279 TYR cc_start: 0.6559 (t80) cc_final: 0.6315 (t80) REVERT: A 290 TYR cc_start: 0.7262 (m-80) cc_final: 0.6567 (m-80) REVERT: A 304 MET cc_start: 0.8606 (ptt) cc_final: 0.7736 (mmt) REVERT: A 314 MET cc_start: 0.8178 (mtt) cc_final: 0.7183 (tpp) REVERT: A 342 ARG cc_start: 0.5802 (ptt180) cc_final: 0.5259 (ptt180) REVERT: A 361 LYS cc_start: 0.8661 (mttt) cc_final: 0.8354 (tppt) REVERT: A 437 ASP cc_start: 0.8440 (t70) cc_final: 0.7848 (t0) REVERT: A 460 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7976 (mmm) REVERT: A 506 MET cc_start: 0.8889 (tpp) cc_final: 0.8237 (ttm) REVERT: A 517 ILE cc_start: 0.8400 (pt) cc_final: 0.8136 (tt) REVERT: A 526 LYS cc_start: 0.7856 (ttpt) cc_final: 0.6702 (pttt) REVERT: A 530 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8066 (mm-30) REVERT: A 587 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8032 (tt) REVERT: A 1018 ARG cc_start: 0.6835 (mpt-90) cc_final: 0.6585 (mpt-90) REVERT: A 1067 MET cc_start: 0.7038 (ptp) cc_final: 0.6740 (ptp) REVERT: B 290 TYR cc_start: 0.7271 (m-80) cc_final: 0.6601 (m-80) REVERT: B 304 MET cc_start: 0.8607 (ptt) cc_final: 0.7731 (mmt) REVERT: B 361 LYS cc_start: 0.8601 (mttt) cc_final: 0.8355 (tppt) REVERT: B 437 ASP cc_start: 0.8612 (t70) cc_final: 0.8283 (t0) REVERT: B 517 ILE cc_start: 0.8441 (pt) cc_final: 0.8173 (tt) REVERT: B 526 LYS cc_start: 0.7735 (ttpt) cc_final: 0.6542 (pttt) REVERT: B 530 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7874 (mm-30) REVERT: B 587 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8028 (tt) REVERT: B 1018 ARG cc_start: 0.7059 (mpt-90) cc_final: 0.6722 (mpt-90) REVERT: B 1067 MET cc_start: 0.7006 (ptp) cc_final: 0.6771 (ptp) REVERT: C 286 SER cc_start: 0.7474 (m) cc_final: 0.7062 (t) REVERT: C 304 MET cc_start: 0.6810 (ppp) cc_final: 0.6541 (ttm) REVERT: C 378 LEU cc_start: 0.8462 (tp) cc_final: 0.8254 (tp) REVERT: C 442 MET cc_start: 0.8677 (mmm) cc_final: 0.8431 (mmp) REVERT: C 479 GLU cc_start: 0.7980 (tm-30) cc_final: 0.6818 (tm-30) REVERT: C 530 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7709 (mm-30) REVERT: C 752 TRP cc_start: 0.8210 (t60) cc_final: 0.7732 (t60) REVERT: C 824 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8140 (tp30) REVERT: C 955 ASP cc_start: 0.7525 (m-30) cc_final: 0.6775 (p0) REVERT: C 960 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: C 983 SER cc_start: 0.8944 (m) cc_final: 0.8481 (p) REVERT: C 1038 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7653 (pp) REVERT: C 1090 TYR cc_start: 0.8420 (p90) cc_final: 0.7917 (p90) REVERT: D 286 SER cc_start: 0.7468 (m) cc_final: 0.7056 (t) REVERT: D 304 MET cc_start: 0.6803 (ppp) cc_final: 0.6537 (ttm) REVERT: D 378 LEU cc_start: 0.8458 (tp) cc_final: 0.8248 (tp) REVERT: D 479 GLU cc_start: 0.7994 (tm-30) cc_final: 0.6830 (tm-30) REVERT: D 530 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7716 (mm-30) REVERT: D 752 TRP cc_start: 0.8195 (t60) cc_final: 0.7727 (t60) REVERT: D 955 ASP cc_start: 0.7526 (m-30) cc_final: 0.6777 (p0) REVERT: D 960 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: D 983 SER cc_start: 0.8930 (m) cc_final: 0.8468 (p) REVERT: D 1038 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7655 (pp) REVERT: D 1090 TYR cc_start: 0.8423 (p90) cc_final: 0.7925 (p90) outliers start: 67 outliers final: 56 residues processed: 307 average time/residue: 0.3138 time to fit residues: 155.2074 Evaluate side-chains 311 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 248 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1038 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108472 restraints weight = 42829.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111622 restraints weight = 24155.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113717 restraints weight = 17324.974| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23452 Z= 0.195 Angle : 0.560 9.261 31816 Z= 0.285 Chirality : 0.044 0.323 3660 Planarity : 0.003 0.038 4040 Dihedral : 4.851 41.211 3116 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 2.83 % Allowed : 14.64 % Favored : 82.54 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2884 helix: -0.83 (0.16), residues: 1110 sheet: -0.99 (0.29), residues: 360 loop : -0.78 (0.18), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 246 HIS 0.003 0.001 HIS C 468 PHE 0.028 0.001 PHE D1070 TYR 0.011 0.001 TYR C 274 ARG 0.004 0.000 ARG D 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.85 seconds wall clock time: 77 minutes 56.52 seconds (4676.52 seconds total)