Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 12:26:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/04_2023/6nd0_0439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/04_2023/6nd0_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_0439/04_2023/6nd0_0439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/04_2023/6nd0_0439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/04_2023/6nd0_0439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd0_0439/04_2023/6nd0_0439.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 11.70, per 1000 atoms: 0.51 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: 9.42 Conformation dependent library (CDL) restraints added in 3.7 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: 1.61 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: 7.68 Time building geometry restraints manager: 10.16 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: 1.380 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: 0.010 Extract box with map and model: 5.880 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 58.980 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.260 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.741 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 outliers start: 11 outliers final: 2 residues processed: 542 average time/residue: 0.3756 time to fit residues: 306.9458 Evaluate side-chains 262 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1952 time to fit residues: 4.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 147 optimal weight: 0.2980 chunk 116 optimal weight: 0.7980 chunk 225 optimal weight: 40.0000 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 751 HIS A 803 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 751 HIS B 803 ASN B 867 ASN B1079 HIS C 379 HIS C 427 ASN C 534 ASN C 585 ASN C 811 HIS C 874 GLN C 942 ASN C 945 ASN D 379 HIS D 427 ASN D 459 GLN D 468 HIS 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2563 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= 0.183 Angle : 0.628 9.568 31816 Z= 0.334 Chirality : 0.044 0.285 3660 Planarity : 0.005 0.045 4040 Dihedral : 6.313 80.885 3116 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.48 % Rotamer Outliers : 1.77 % 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: -3.45 (0.14), residues: 2884 helix: -3.04 (0.12), residues: 1076 sheet: -1.51 (0.25), residues: 396 loop : -1.78 (0.16), residues: 1412 *********************** 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 373 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 328 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 361 average time/residue: 0.3849 time to fit residues: 212.0627 Evaluate side-chains 270 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 2.879 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3585 time to fit residues: 16.5809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 262 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 ASN B 468 HIS ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN C 459 GLN C 805 HIS D 459 GLN D 805 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 23452 Z= 0.451 Angle : 0.715 7.179 31816 Z= 0.376 Chirality : 0.048 0.296 3660 Planarity : 0.005 0.044 4040 Dihedral : 6.410 77.880 3116 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % Favored : 91.99 % Rotamer Outliers : 1.84 % 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: -2.97 (0.15), residues: 2884 helix: -2.49 (0.13), residues: 1098 sheet: -1.17 (0.26), residues: 378 loop : -1.66 (0.17), residues: 1408 *********************** 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 301 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 289 average time/residue: 0.3423 time to fit residues: 156.3484 Evaluate side-chains 254 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 2.798 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2149 time to fit residues: 17.7363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3551 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= 0.166 Angle : 0.553 9.033 31816 Z= 0.290 Chirality : 0.043 0.226 3660 Planarity : 0.004 0.041 4040 Dihedral : 5.691 74.460 3116 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer Outliers : 0.86 % 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: -2.51 (0.15), residues: 2884 helix: -2.03 (0.14), residues: 1102 sheet: -0.93 (0.26), residues: 396 loop : -1.45 (0.17), residues: 1386 *********************** 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 293 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 271 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 6 residues processed: 283 average time/residue: 0.3428 time to fit residues: 153.5175 Evaluate side-chains 247 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2042 time to fit residues: 5.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 207 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- 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** C 231 ASN D 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3757 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= 0.280 Angle : 0.590 8.011 31816 Z= 0.306 Chirality : 0.045 0.292 3660 Planarity : 0.004 0.039 4040 Dihedral : 5.668 76.366 3116 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2884 helix: -1.68 (0.14), residues: 1068 sheet: -0.90 (0.27), residues: 396 loop : -1.30 (0.17), residues: 1420 *********************** 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 300 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 29 residues processed: 278 average time/residue: 0.3559 time to fit residues: 158.6042 Evaluate side-chains 260 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2158 time to fit residues: 15.7446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 278 optimal weight: 0.0050 chunk 231 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 GLN B 942 ASN C 365 HIS D 365 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23452 Z= 0.177 Angle : 0.544 7.541 31816 Z= 0.282 Chirality : 0.044 0.282 3660 Planarity : 0.003 0.038 4040 Dihedral : 5.346 74.162 3116 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer Outliers : 0.94 % 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: -1.81 (0.16), residues: 2884 helix: -1.35 (0.15), residues: 1072 sheet: -0.75 (0.27), residues: 396 loop : -1.08 (0.17), residues: 1416 *********************** 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 276 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 3.034 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 266 average time/residue: 0.3463 time to fit residues: 147.7808 Evaluate side-chains 235 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 2.745 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2152 time to fit residues: 8.2514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 128 optimal weight: 0.0470 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN B 794 ASN ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 23452 Z= 0.162 Angle : 0.539 8.933 31816 Z= 0.277 Chirality : 0.044 0.317 3660 Planarity : 0.003 0.038 4040 Dihedral : 5.135 72.685 3116 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.79 % Favored : 94.14 % Rotamer Outliers : 0.67 % 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: -1.63 (0.16), residues: 2884 helix: -1.15 (0.15), residues: 1086 sheet: -0.70 (0.27), residues: 396 loop : -1.02 (0.18), residues: 1402 *********************** 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 263 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 255 average time/residue: 0.3476 time to fit residues: 143.2155 Evaluate side-chains 229 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2253 time to fit residues: 6.7803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 218 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 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: 0.7353 moved from start: 0.4261 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= 0.174 Angle : 0.547 9.841 31816 Z= 0.281 Chirality : 0.044 0.307 3660 Planarity : 0.003 0.038 4040 Dihedral : 5.074 72.380 3116 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer Outliers : 0.86 % 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: -1.52 (0.16), residues: 2884 helix: -1.01 (0.15), residues: 1084 sheet: -0.83 (0.28), residues: 362 loop : -0.93 (0.18), residues: 1438 *********************** 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 256 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 2.801 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 249 average time/residue: 0.3489 time to fit residues: 139.5898 Evaluate side-chains 234 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 223 time to evaluate : 2.904 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2201 time to fit residues: 8.1837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 155 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 244 optimal weight: 0.0770 chunk 257 optimal weight: 3.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 803 ASN C 365 HIS D 365 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 23452 Z= 0.149 Angle : 0.546 9.860 31816 Z= 0.279 Chirality : 0.044 0.305 3660 Planarity : 0.003 0.038 4040 Dihedral : 4.905 70.467 3116 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.44 % Favored : 94.49 % Rotamer Outliers : 0.75 % 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: -1.39 (0.16), residues: 2884 helix: -0.90 (0.16), residues: 1108 sheet: -0.74 (0.29), residues: 360 loop : -0.86 (0.18), residues: 1416 *********************** 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 279 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 272 average time/residue: 0.3545 time to fit residues: 152.3668 Evaluate side-chains 245 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2375 time to fit residues: 8.0230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.4980 chunk 273 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 874 GLN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23452 Z= 0.203 Angle : 0.570 9.907 31816 Z= 0.292 Chirality : 0.045 0.317 3660 Planarity : 0.003 0.038 4040 Dihedral : 5.030 72.190 3116 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer Outliers : 0.39 % 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: -1.24 (0.16), residues: 2884 helix: -0.76 (0.16), residues: 1076 sheet: -0.73 (0.28), residues: 368 loop : -0.77 (0.18), residues: 1440 ********************** 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 243 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 238 average time/residue: 0.3514 time to fit residues: 133.6463 Evaluate side-chains 229 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 2.721 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2299 time to fit residues: 6.6077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN C 874 GLN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110514 restraints weight = 42550.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113175 restraints weight = 26725.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114143 restraints weight = 19332.348| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23452 Z= 0.214 Angle : 0.581 9.567 31816 Z= 0.297 Chirality : 0.045 0.313 3660 Planarity : 0.003 0.038 4040 Dihedral : 5.107 73.721 3116 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer Outliers : 0.31 % 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: -1.29 (0.16), residues: 2884 helix: -0.80 (0.16), residues: 1086 sheet: -0.79 (0.29), residues: 360 loop : -0.78 (0.18), residues: 1438 =============================================================================== Job complete usr+sys time: 4040.54 seconds wall clock time: 75 minutes 11.05 seconds (4511.05 seconds total)