Starting phenix.real_space_refine on Fri Sep 27 02:24:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqb_22993/09_2024/7kqb_22993_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqb_22993/09_2024/7kqb_22993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqb_22993/09_2024/7kqb_22993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqb_22993/09_2024/7kqb_22993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqb_22993/09_2024/7kqb_22993_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kqb_22993/09_2024/7kqb_22993_trim.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.075 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: 5 Type Number sf(0) Gaussians S 140 5.16 5 C 20465 2.51 5 N 5356 2.21 5 O 6254 1.98 5 H 31094 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63309 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 16699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 16699 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 54, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 16677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 16677 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 54, 'TRANS': 1024} Chain breaks: 5 Chain: "C" Number of atoms: 16661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 16661 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Chain: "H" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3257 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "L" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3218 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "K" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3257 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "J" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3218 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 22.30, per 1000 atoms: 0.35 Number of scatterers: 63309 At special positions: 0 Unit cell: (185.259, 161.508, 230.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 O 6254 8.00 N 5356 7.00 C 20465 6.00 H 31094 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.02 Simple disulfide: pdb=" SG CYS H 222 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.00 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 202 " distance=2.03 Simple disulfide: pdb=" SG CYS K 222 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.06 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 3.8 seconds 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7656 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 76 sheets defined 22.6% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.947A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.627A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.583A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.746A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.866A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.500A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.730A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.013A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 removed outlier: 4.430A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.876A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.711A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.637A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.774A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.564A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.709A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.100A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.383A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.594A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.693A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.366A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.249A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 624 Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.783A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.760A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.628A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.795A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.068A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.745A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.173A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.272A pdb=" N GLY H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 210 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 removed outlier: 4.400A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 191 through 197 removed outlier: 3.912A pdb=" N GLY K 196 " --> pdb=" O SER K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 210 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.899A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 126 removed outlier: 3.760A pdb=" N LYS J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 183 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.037A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.518A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.708A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.091A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.933A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.370A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.186A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.456A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.614A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.996A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.817A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.974A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 158 through 171 removed outlier: 7.418A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 154 removed outlier: 12.754A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.455A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.761A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.440A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.439A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.549A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.549A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.781A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.435A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.435A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.506A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.936A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.658A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.337A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.248A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.055A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.562A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.728A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.105A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.519A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.519A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.568A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.661A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.540A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.746A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.746A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 201 through 202 Processing sheet with id=AG2, first strand: chain 'H' and resid 205 through 206 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.429A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.969A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AG7, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AG8, first strand: chain 'L' and resid 137 through 139 removed outlier: 4.823A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 145 through 148 Processing sheet with id=AH1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.623A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.716A pdb=" N TYR K 108 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 126 through 129 removed outlier: 4.934A pdb=" N GLY K 145 " --> pdb=" O VAL K 188 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL K 188 " --> pdb=" O GLY K 145 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU K 147 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER K 186 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS K 149 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU K 184 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER K 183 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA K 174 " --> pdb=" O SER K 183 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER K 185 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 201 through 202 Processing sheet with id=AH6, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AH7, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.338A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.148A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 117 through 118 Processing sheet with id=AI2, first strand: chain 'J' and resid 129 through 131 Processing sheet with id=AI3, first strand: chain 'J' and resid 145 through 148 Processing sheet with id=AI4, first strand: chain 'J' and resid 160 through 164 removed outlier: 3.934A pdb=" N SER J 174 " --> pdb=" O THR J 164 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 3624 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: 27.67 Time building geometry restraints manager: 15.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 31094 1.13 - 1.31: 5591 1.31 - 1.48: 13284 1.48 - 1.65: 13902 1.65 - 1.83: 176 Bond restraints: 64047 Sorted by residual: bond pdb=" CD1 PHE A 486 " pdb=" HD1 PHE A 486 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS A 310 " pdb=" H LYS A 310 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CZ PHE C 802 " pdb=" HZ PHE C 802 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 TYR A 612 " pdb=" HE1 TYR A 612 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CZ3 TRP B 633 " pdb=" HZ3 TRP B 633 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 64042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 89948 2.10 - 4.21: 18998 4.21 - 6.31: 4821 6.31 - 8.42: 1410 8.42 - 10.52: 46 Bond angle restraints: 115223 Sorted by residual: angle pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " pdb=" CG ASN A 122 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.08 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" C LYS K 215 " pdb=" N LYS K 216 " pdb=" CA LYS K 216 " ideal model delta sigma weight residual 120.82 129.53 -8.71 1.41e+00 5.03e-01 3.82e+01 angle pdb=" CA ASP B 808 " pdb=" CB ASP B 808 " pdb=" CG ASP B 808 " ideal model delta sigma weight residual 112.60 118.77 -6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" CA GLY C 416 " pdb=" C GLY C 416 " pdb=" N LYS C 417 " ideal model delta sigma weight residual 114.23 119.56 -5.33 8.80e-01 1.29e+00 3.67e+01 ... (remaining 115218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 28086 17.98 - 35.96: 1792 35.96 - 53.94: 612 53.94 - 71.92: 585 71.92 - 89.90: 44 Dihedral angle restraints: 31119 sinusoidal: 16870 harmonic: 14249 Sorted by residual: dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual -86.00 -139.79 53.79 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA PRO B 589 " pdb=" C PRO B 589 " pdb=" N CYS B 590 " pdb=" CA CYS B 590 " ideal model delta harmonic sigma weight residual 180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA TYR B 612 " pdb=" C TYR B 612 " pdb=" N GLN B 613 " pdb=" CA GLN B 613 " ideal model delta harmonic sigma weight residual 180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 31116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3475 0.098 - 0.196: 1446 0.196 - 0.294: 172 0.294 - 0.392: 36 0.392 - 0.490: 8 Chirality restraints: 5137 Sorted by residual: chirality pdb=" CA TYR B 636 " pdb=" N TYR B 636 " pdb=" C TYR B 636 " pdb=" CB TYR B 636 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA LEU A 977 " pdb=" N LEU A 977 " pdb=" C LEU A 977 " pdb=" CB LEU A 977 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA CYS B 590 " pdb=" N CYS B 590 " pdb=" C CYS B 590 " pdb=" CB CYS B 590 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 5134 not shown) Planarity restraints: 9673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 160 " -0.369 2.00e-02 2.50e+03 1.41e-01 7.96e+02 pdb=" CG TRP H 160 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP H 160 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP H 160 " 0.114 2.00e-02 2.50e+03 pdb=" NE1 TRP H 160 " 0.126 2.00e-02 2.50e+03 pdb=" CE2 TRP H 160 " 0.079 2.00e-02 2.50e+03 pdb=" CE3 TRP H 160 " 0.126 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 160 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 160 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP H 160 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 TRP H 160 " -0.085 2.00e-02 2.50e+03 pdb=" HE1 TRP H 160 " 0.145 2.00e-02 2.50e+03 pdb=" HE3 TRP H 160 " 0.160 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 160 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 160 " 0.066 2.00e-02 2.50e+03 pdb=" HH2 TRP H 160 " -0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 160 " -0.257 2.00e-02 2.50e+03 1.05e-01 4.37e+02 pdb=" CG TRP K 160 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP K 160 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP K 160 " 0.127 2.00e-02 2.50e+03 pdb=" NE1 TRP K 160 " 0.113 2.00e-02 2.50e+03 pdb=" CE2 TRP K 160 " 0.092 2.00e-02 2.50e+03 pdb=" CE3 TRP K 160 " 0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 160 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 160 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP K 160 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TRP K 160 " -0.113 2.00e-02 2.50e+03 pdb=" HE1 TRP K 160 " 0.043 2.00e-02 2.50e+03 pdb=" HE3 TRP K 160 " 0.113 2.00e-02 2.50e+03 pdb=" HZ2 TRP K 160 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP K 160 " -0.039 2.00e-02 2.50e+03 pdb=" HH2 TRP K 160 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 118 " 0.269 2.00e-02 2.50e+03 1.11e-01 3.68e+02 pdb=" CG PHE L 118 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE L 118 " -0.110 2.00e-02 2.50e+03 pdb=" CD2 PHE L 118 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 PHE L 118 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE L 118 " -0.043 2.00e-02 2.50e+03 pdb=" CZ PHE L 118 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE L 118 " -0.093 2.00e-02 2.50e+03 pdb=" HD2 PHE L 118 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE L 118 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE L 118 " -0.056 2.00e-02 2.50e+03 pdb=" HZ PHE L 118 " 0.191 2.00e-02 2.50e+03 ... (remaining 9670 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3783 2.16 - 2.77: 108498 2.77 - 3.38: 180709 3.38 - 3.99: 247850 3.99 - 4.60: 358934 Nonbonded interactions: 899774 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" HG SER B 366 " model vdw 1.550 2.450 nonbonded pdb=" OD1 ASP A 985 " pdb=" HG SER C 383 " model vdw 1.576 2.450 nonbonded pdb=" HG SER C 746 " pdb=" OE1 GLU C 748 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP C 364 " pdb=" HG SER C 366 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP C 253 " pdb=" HG SER C 256 " model vdw 1.583 2.450 ... (remaining 899769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1073 or (resid 1074 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 1075 \ through 1146 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 332 through 342 or (resid 343 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 344 \ through 624 or resid 633 through 826 or resid 855 through 1073 or (resid 1074 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 107 \ 5 through 1097 or (resid 1098 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name \ HB3 or name HD21)) or resid 1099 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 332 through 624 or resid 633 th \ rough 708 or (resid 709 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or \ name HD21)) or resid 710 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.410 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: 0.840 Extract box with map and model: 1.940 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 108.410 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.190 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:10.080 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 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 : 0.012 0.073 32953 Z= 0.816 Angle : 1.789 10.213 44842 Z= 1.190 Chirality : 0.100 0.490 5137 Planarity : 0.015 0.219 5773 Dihedral : 13.665 89.895 12154 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.34 % Favored : 94.43 % Rotamer: Outliers : 1.23 % Allowed : 4.95 % Favored : 93.82 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.97 % 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: -1.06 (0.12), residues: 4061 helix: -0.55 (0.17), residues: 698 sheet: 0.14 (0.16), residues: 944 loop : -1.10 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.250 0.031 TRP H 160 HIS 0.020 0.004 HIS K 206 PHE 0.157 0.012 PHE L 118 TYR 0.184 0.020 TYR J 140 ARG 0.014 0.002 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 93 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.9213 (ptm) cc_final: 0.8979 (ptm) REVERT: A 900 MET cc_start: 0.8979 (mtp) cc_final: 0.8672 (ttm) REVERT: A 935 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: B 177 MET cc_start: 0.7452 (ptp) cc_final: 0.7169 (ptp) REVERT: K 141 THR cc_start: 0.4389 (OUTLIER) cc_final: 0.4142 (p) outliers start: 44 outliers final: 12 residues processed: 135 average time/residue: 2.5809 time to fit residues: 420.8957 Evaluate side-chains 73 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 141 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 238 optimal weight: 40.0000 chunk 370 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 764 ASN A 824 ASN A1023 ASN A1088 HIS B 125 ASN B 487 ASN C 439 ASN C 641 ASN C 779 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32953 Z= 0.243 Angle : 0.695 7.576 44842 Z= 0.381 Chirality : 0.046 0.242 5137 Planarity : 0.005 0.074 5773 Dihedral : 7.794 77.677 4916 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.15 % Allowed : 6.44 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4061 helix: 0.69 (0.19), residues: 693 sheet: -0.20 (0.15), residues: 1078 loop : -1.01 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 633 HIS 0.011 0.001 HIS H 206 PHE 0.016 0.001 PHE L 116 TYR 0.040 0.002 TYR J 186 ARG 0.005 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 64 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 900 MET cc_start: 0.8964 (mtp) cc_final: 0.8657 (ttm) REVERT: C 200 TYR cc_start: 0.8367 (m-80) cc_final: 0.8013 (m-80) outliers start: 41 outliers final: 12 residues processed: 100 average time/residue: 2.3561 time to fit residues: 293.2487 Evaluate side-chains 70 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 169 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 40.0000 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A 935 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN C 919 ASN H 57 ASN H 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 32953 Z= 0.347 Angle : 0.617 7.346 44842 Z= 0.335 Chirality : 0.045 0.225 5137 Planarity : 0.004 0.071 5773 Dihedral : 6.658 58.899 4896 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.76 % Allowed : 7.36 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4061 helix: 1.01 (0.20), residues: 692 sheet: -0.35 (0.15), residues: 1086 loop : -0.98 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 633 HIS 0.008 0.001 HIS H 206 PHE 0.018 0.001 PHE B 318 TYR 0.025 0.002 TYR J 186 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 55 time to evaluate : 3.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8954 (mtp) cc_final: 0.8632 (ttm) REVERT: B 177 MET cc_start: 0.7404 (ptp) cc_final: 0.6847 (pmm) REVERT: C 66 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7830 (p90) REVERT: C 200 TYR cc_start: 0.8496 (m-80) cc_final: 0.8230 (m-80) REVERT: C 572 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8554 (p) outliers start: 27 outliers final: 10 residues processed: 79 average time/residue: 2.3143 time to fit residues: 227.5630 Evaluate side-chains 66 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain J residue 161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 6.9990 chunk 279 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 353 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN A1064 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32953 Z= 0.197 Angle : 0.552 7.323 44842 Z= 0.296 Chirality : 0.043 0.191 5137 Planarity : 0.004 0.071 5773 Dihedral : 6.203 56.912 4896 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.67 % Allowed : 7.97 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4061 helix: 1.52 (0.21), residues: 675 sheet: -0.36 (0.15), residues: 1092 loop : -0.90 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.005 0.001 HIS H 206 PHE 0.011 0.001 PHE B 318 TYR 0.019 0.001 TYR J 186 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8912 (mtp) cc_final: 0.8570 (ttm) REVERT: B 177 MET cc_start: 0.7303 (ptp) cc_final: 0.6837 (pmm) REVERT: C 66 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7693 (p90) REVERT: C 200 TYR cc_start: 0.8503 (m-80) cc_final: 0.8275 (m-80) REVERT: C 572 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8551 (p) outliers start: 24 outliers final: 10 residues processed: 81 average time/residue: 2.3491 time to fit residues: 235.2389 Evaluate side-chains 67 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain J residue 161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 336 optimal weight: 50.0000 chunk 272 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 703 ASN H 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32953 Z= 0.355 Angle : 0.570 6.199 44842 Z= 0.306 Chirality : 0.044 0.218 5137 Planarity : 0.004 0.070 5773 Dihedral : 6.025 57.555 4896 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.95 % Allowed : 8.37 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4061 helix: 1.53 (0.21), residues: 669 sheet: -0.48 (0.15), residues: 1103 loop : -0.94 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 160 HIS 0.004 0.001 HIS H 206 PHE 0.020 0.001 PHE B 318 TYR 0.020 0.001 TYR B1067 ARG 0.010 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 56 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: A 900 MET cc_start: 0.8957 (mtp) cc_final: 0.8636 (ttm) REVERT: B 177 MET cc_start: 0.7177 (ptp) cc_final: 0.6792 (pmm) REVERT: C 66 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7696 (p90) REVERT: C 153 MET cc_start: 0.8265 (pmm) cc_final: 0.7313 (pmm) REVERT: C 572 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8537 (p) REVERT: L 134 CYS cc_start: 0.3861 (OUTLIER) cc_final: 0.3558 (m) outliers start: 34 outliers final: 12 residues processed: 88 average time/residue: 2.1902 time to fit residues: 242.3201 Evaluate side-chains 69 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain J residue 161 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 8.9990 chunk 327 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32953 Z= 0.302 Angle : 0.552 8.998 44842 Z= 0.295 Chirality : 0.043 0.208 5137 Planarity : 0.004 0.075 5773 Dihedral : 5.854 57.749 4895 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.64 % Allowed : 8.76 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4061 helix: 1.63 (0.20), residues: 669 sheet: -0.48 (0.15), residues: 1089 loop : -0.92 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.004 0.001 HIS H 206 PHE 0.014 0.001 PHE B 318 TYR 0.019 0.001 TYR J 186 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: A 900 MET cc_start: 0.8945 (mtp) cc_final: 0.8591 (ttm) REVERT: B 177 MET cc_start: 0.7174 (ptp) cc_final: 0.6786 (pmm) REVERT: C 66 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7632 (p90) REVERT: C 146 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: C 153 MET cc_start: 0.8080 (pmm) cc_final: 0.7544 (pmm) REVERT: C 572 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8541 (p) REVERT: L 104 LEU cc_start: 0.1877 (OUTLIER) cc_final: 0.1462 (tp) outliers start: 23 outliers final: 8 residues processed: 75 average time/residue: 2.3187 time to fit residues: 218.1562 Evaluate side-chains 65 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 288 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 580 GLN B1135 ASN C 787 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 32953 Z= 0.460 Angle : 0.595 6.499 44842 Z= 0.319 Chirality : 0.045 0.246 5137 Planarity : 0.004 0.072 5773 Dihedral : 5.896 59.115 4895 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.78 % Allowed : 8.79 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4061 helix: 1.27 (0.20), residues: 688 sheet: -0.58 (0.15), residues: 1081 loop : -1.04 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 160 HIS 0.007 0.001 HIS B 245 PHE 0.020 0.002 PHE B 318 TYR 0.021 0.002 TYR B1067 ARG 0.004 0.001 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 52 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: A 900 MET cc_start: 0.8974 (mtp) cc_final: 0.8663 (ttm) REVERT: C 66 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7640 (p90) REVERT: C 515 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7504 (p90) REVERT: C 564 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8424 (mm110) REVERT: H 34 MET cc_start: 0.4568 (mmm) cc_final: 0.3954 (mmm) REVERT: L 104 LEU cc_start: 0.1934 (OUTLIER) cc_final: 0.1537 (tp) outliers start: 28 outliers final: 15 residues processed: 79 average time/residue: 2.2511 time to fit residues: 223.1903 Evaluate side-chains 71 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 40.0000 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 0.3980 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN C 787 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32953 Z= 0.158 Angle : 0.512 6.187 44842 Z= 0.273 Chirality : 0.043 0.187 5137 Planarity : 0.004 0.071 5773 Dihedral : 5.577 57.206 4895 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.59 % Allowed : 8.98 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4061 helix: 1.88 (0.21), residues: 662 sheet: -0.46 (0.15), residues: 1077 loop : -0.89 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 633 HIS 0.005 0.001 HIS A1088 PHE 0.012 0.001 PHE C 898 TYR 0.016 0.001 TYR J 186 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 3.945 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 180 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: A 900 MET cc_start: 0.8910 (mtp) cc_final: 0.8580 (ttm) REVERT: B 177 MET cc_start: 0.7274 (ptp) cc_final: 0.6434 (pmm) REVERT: C 66 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7494 (p90) REVERT: C 153 MET cc_start: 0.8330 (pmm) cc_final: 0.7692 (pmm) REVERT: C 564 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8456 (mm110) REVERT: C 572 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8503 (p) REVERT: H 34 MET cc_start: 0.4481 (mmm) cc_final: 0.3850 (mmm) REVERT: L 104 LEU cc_start: 0.1920 (OUTLIER) cc_final: 0.1507 (tp) outliers start: 21 outliers final: 9 residues processed: 73 average time/residue: 2.4270 time to fit residues: 220.0388 Evaluate side-chains 64 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 50.0000 chunk 376 optimal weight: 0.7980 chunk 343 optimal weight: 6.9990 chunk 366 optimal weight: 0.3980 chunk 220 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 20.0000 chunk 365 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32953 Z= 0.199 Angle : 0.502 6.709 44842 Z= 0.267 Chirality : 0.042 0.186 5137 Planarity : 0.004 0.070 5773 Dihedral : 5.376 54.472 4895 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.45 % Allowed : 9.29 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4061 helix: 1.99 (0.21), residues: 662 sheet: -0.42 (0.15), residues: 1079 loop : -0.84 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 160 HIS 0.004 0.001 HIS A1088 PHE 0.011 0.001 PHE C 898 TYR 0.016 0.001 TYR J 186 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 3.914 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 180 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: A 900 MET cc_start: 0.8942 (mtp) cc_final: 0.8630 (ttm) REVERT: B 177 MET cc_start: 0.7155 (ptp) cc_final: 0.6402 (pmm) REVERT: C 66 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7491 (p90) REVERT: C 153 MET cc_start: 0.8315 (pmm) cc_final: 0.7638 (pmm) REVERT: C 572 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8499 (p) REVERT: H 34 MET cc_start: 0.4287 (mmm) cc_final: 0.3812 (mmm) REVERT: L 104 LEU cc_start: 0.1942 (OUTLIER) cc_final: 0.1552 (tp) outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 2.3709 time to fit residues: 189.8338 Evaluate side-chains 61 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 4.9990 chunk 387 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN B1088 HIS H 39 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 32953 Z= 0.400 Angle : 0.549 5.998 44842 Z= 0.293 Chirality : 0.044 0.224 5137 Planarity : 0.004 0.069 5773 Dihedral : 5.507 57.613 4894 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.48 % Allowed : 9.37 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4061 helix: 1.78 (0.21), residues: 668 sheet: -0.49 (0.15), residues: 1081 loop : -0.93 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 160 HIS 0.005 0.001 HIS B 245 PHE 0.016 0.001 PHE B 318 TYR 0.019 0.001 TYR B1067 ARG 0.011 0.000 ARG J 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8989 (mtp) cc_final: 0.8685 (ttm) REVERT: B 177 MET cc_start: 0.7234 (ptp) cc_final: 0.6438 (pmm) REVERT: C 66 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7455 (p90) REVERT: C 153 MET cc_start: 0.8472 (pmm) cc_final: 0.7817 (pmm) REVERT: L 104 LEU cc_start: 0.2010 (OUTLIER) cc_final: 0.1614 (tp) outliers start: 17 outliers final: 12 residues processed: 63 average time/residue: 2.4352 time to fit residues: 193.7967 Evaluate side-chains 62 residues out of total 3574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 580 GLN H 39 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.071561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.044748 restraints weight = 433068.333| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.20 r_work: 0.2999 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32953 Z= 0.168 Angle : 0.497 5.710 44842 Z= 0.264 Chirality : 0.042 0.181 5137 Planarity : 0.004 0.069 5773 Dihedral : 5.321 55.593 4894 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.53 % Allowed : 9.32 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4061 helix: 2.01 (0.21), residues: 662 sheet: -0.42 (0.15), residues: 1081 loop : -0.84 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 160 HIS 0.004 0.001 HIS A1088 PHE 0.011 0.001 PHE C 898 TYR 0.015 0.001 TYR C 369 ARG 0.006 0.000 ARG J 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12139.59 seconds wall clock time: 210 minutes 43.55 seconds (12643.55 seconds total)