Starting phenix.real_space_refine on Thu May 29 06:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yww_39645/05_2025/8yww_39645_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yww_39645/05_2025/8yww_39645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yww_39645/05_2025/8yww_39645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yww_39645/05_2025/8yww_39645.map" model { file = "/net/cci-nas-00/data/ceres_data/8yww_39645/05_2025/8yww_39645_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yww_39645/05_2025/8yww_39645_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 20186 2.51 5 N 5300 2.21 5 O 6027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31649 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1619 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1646 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "F" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1646 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1619 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "H" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1857 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 235} Time building chain proxies: 16.96, per 1000 atoms: 0.54 Number of scatterers: 31649 At special positions: 0 Unit cell: (145.658, 145.658, 252.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 6027 8.00 N 5300 7.00 C 20186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 227 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.62 Conformation dependent library (CDL) restraints added in 4.1 seconds 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7758 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 69 sheets defined 20.1% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.872A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.235A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.543A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.532A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.120A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.916A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.516A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (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 983 removed outlier: 3.783A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.191A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.872A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.235A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.543A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.590A 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 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.079A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.957A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 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 removed outlier: 3.724A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.141A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.006A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.614A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.517A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.644A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 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 983 removed outlier: 3.767A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.049A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.581A pdb=" N ASN E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.580A pdb=" N LYS E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.163A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.163A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.581A pdb=" N ASN G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.580A pdb=" N LYS G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.729A pdb=" N ASP H 31 " --> pdb=" O LYS H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.534A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.292A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.924A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.722A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.082A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.125A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.033A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.721A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.721A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.887A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.790A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.653A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.041A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.597A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.363A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.033A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.102A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.700A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.469A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.852A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.728A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.556A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.933A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.929A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.748A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.093A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.628A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.628A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.231A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.826A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 18 through 21 removed outlier: 3.628A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 94 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 106 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 94 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA E 141 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 188 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA E 141 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 188 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER E 181 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 173 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 154 through 158 removed outlier: 3.554A pdb=" N THR E 155 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR E 198 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 211 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.694A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.743A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS D 107 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA D 13 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 86 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.927A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 134 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 176 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN D 160 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.210A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN D 147 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D 195 " --> pdb=" O GLN D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 149 through 150 Processing sheet with id=AG1, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.693A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.743A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS F 107 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA F 13 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR F 86 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.927A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 134 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 176 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN F 160 " --> pdb=" O THR F 178 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 145 through 147 removed outlier: 4.210A pdb=" N LYS F 145 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 197 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN F 147 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU F 195 " --> pdb=" O GLN F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 149 through 150 Processing sheet with id=AG6, first strand: chain 'G' and resid 18 through 21 removed outlier: 3.628A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 94 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 106 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 94 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 181 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL G 173 " --> pdb=" O SER G 181 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 154 through 158 removed outlier: 3.554A pdb=" N THR G 155 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR G 198 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL G 211 " --> pdb=" O VAL G 202 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.298A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 144 through 146 removed outlier: 3.524A pdb=" N ASP H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 184 through 187 removed outlier: 6.582A pdb=" N TRP H 174 " --> pdb=" O LEU H 186 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3291 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: 16.41 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.71 - 1.17: 3 1.17 - 1.62: 32213 1.62 - 2.08: 172 2.08 - 2.53: 2 2.53 - 2.99: 2 Bond restraints: 32392 Sorted by residual: bond pdb=" C THR A 333 " pdb=" N ASN A 334 " ideal model delta sigma weight residual 1.330 2.986 -1.656 1.39e-02 5.18e+03 1.42e+04 bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.333 2.754 -1.421 1.44e-02 4.82e+03 9.73e+03 bond pdb=" C PRO C 330 " pdb=" N ASN C 331 " ideal model delta sigma weight residual 1.334 1.977 -0.643 1.33e-02 5.65e+03 2.34e+03 bond pdb=" C PRO A 330 " pdb=" N ASN A 331 " ideal model delta sigma weight residual 1.333 2.114 -0.781 1.73e-02 3.34e+03 2.04e+03 bond pdb=" C LYS C 529 " pdb=" N SER C 530 " ideal model delta sigma weight residual 1.332 0.713 0.619 1.40e-02 5.10e+03 1.96e+03 ... (remaining 32387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 23.49: 44139 23.49 - 46.98: 23 46.98 - 70.47: 3 70.47 - 93.95: 1 93.95 - 117.44: 3 Bond angle restraints: 44169 Sorted by residual: angle pdb=" O GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 121.77 4.33 117.44 1.00e+00 1.00e+00 1.38e+04 angle pdb=" CA LYS C 529 " pdb=" C LYS C 529 " pdb=" N SER C 530 " ideal model delta sigma weight residual 116.84 13.09 103.75 1.71e+00 3.42e-01 3.68e+03 angle pdb=" C LYS C 529 " pdb=" N SER C 530 " pdb=" CA SER C 530 " ideal model delta sigma weight residual 121.54 24.66 96.88 1.91e+00 2.74e-01 2.57e+03 angle pdb=" O LYS B 529 " pdb=" C LYS B 529 " pdb=" N SER B 530 " ideal model delta sigma weight residual 122.59 64.13 58.46 1.33e+00 5.65e-01 1.93e+03 angle pdb=" O LYS A 529 " pdb=" C LYS A 529 " pdb=" N SER A 530 " ideal model delta sigma weight residual 122.59 70.63 51.96 1.33e+00 5.65e-01 1.53e+03 ... (remaining 44164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17582 17.95 - 35.90: 1310 35.90 - 53.85: 223 53.85 - 71.80: 64 71.80 - 89.75: 28 Dihedral angle restraints: 19207 sinusoidal: 7120 harmonic: 12087 Sorted by residual: dihedral pdb=" C LEU G 11 " pdb=" N LEU G 11 " pdb=" CA LEU G 11 " pdb=" CB LEU G 11 " ideal model delta harmonic sigma weight residual -122.60 -61.84 -60.76 0 2.50e+00 1.60e-01 5.91e+02 dihedral pdb=" C LEU E 11 " pdb=" N LEU E 11 " pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " ideal model delta harmonic sigma weight residual -122.60 -61.86 -60.74 0 2.50e+00 1.60e-01 5.90e+02 dihedral pdb=" N LEU G 11 " pdb=" C LEU G 11 " pdb=" CA LEU G 11 " pdb=" CB LEU G 11 " ideal model delta harmonic sigma weight residual 122.80 62.54 60.26 0 2.50e+00 1.60e-01 5.81e+02 ... (remaining 19204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4867 0.175 - 0.350: 127 0.350 - 0.525: 35 0.525 - 0.700: 6 0.700 - 0.875: 8 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CA PHE A 338 " pdb=" N PHE A 338 " pdb=" C PHE A 338 " pdb=" CB PHE A 338 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA PHE B 338 " pdb=" N PHE B 338 " pdb=" C PHE B 338 " pdb=" CB PHE B 338 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA SER E 30 " pdb=" N SER E 30 " pdb=" C SER E 30 " pdb=" CB SER E 30 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 ... (remaining 5040 not shown) Planarity restraints: 5728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " -0.112 2.00e-02 2.50e+03 2.04e-01 4.17e+02 pdb=" C GLY C 526 " 0.346 2.00e-02 2.50e+03 pdb=" O GLY C 526 " -0.175 2.00e-02 2.50e+03 pdb=" N PRO C 527 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 333 " -0.111 2.00e-02 2.50e+03 1.68e-01 2.83e+02 pdb=" C THR A 333 " 0.286 2.00e-02 2.50e+03 pdb=" O THR A 333 " -0.131 2.00e-02 2.50e+03 pdb=" N ASN A 334 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 529 " -0.117 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" C LYS B 529 " 0.255 2.00e-02 2.50e+03 pdb=" O LYS B 529 " -0.030 2.00e-02 2.50e+03 pdb=" N SER B 530 " -0.108 2.00e-02 2.50e+03 ... (remaining 5725 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 8 1.46 - 2.32: 118 2.32 - 3.18: 27075 3.18 - 4.04: 77222 4.04 - 4.90: 141908 Warning: very small nonbonded interaction distances. Nonbonded interactions: 246331 Sorted by model distance: nonbonded pdb=" OD2 ASP B 364 " pdb=" CG PRO B 527 " model vdw 0.602 3.440 nonbonded pdb=" OD2 ASP A 364 " pdb=" CD PRO A 527 " model vdw 0.909 3.440 nonbonded pdb=" OD2 ASP A 364 " pdb=" CG PRO A 527 " model vdw 1.062 3.440 nonbonded pdb=" C THR C 333 " pdb=" CB ASN C 334 " model vdw 1.129 3.670 nonbonded pdb=" N THR C 333 " pdb=" CG ASN C 334 " model vdw 1.254 2.680 ... (remaining 246326 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.390 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: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 72.000 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.160 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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 : 0.016 1.656 32443 Z= 1.139 Angle : 1.900 117.442 44267 Z= 1.279 Chirality : 0.082 0.875 5043 Planarity : 0.009 0.204 5728 Dihedral : 13.250 89.750 11302 Min Nonbonded Distance : 0.602 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 0.77 % Allowed : 1.18 % Favored : 98.05 % Cbeta Deviations : 2.37 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 4103 helix: 2.34 (0.21), residues: 660 sheet: 0.15 (0.15), residues: 1079 loop : -1.28 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 353 HIS 0.006 0.001 HIS E 102 PHE 0.020 0.002 PHE B 400 TYR 0.029 0.002 TYR B 453 ARG 0.005 0.001 ARG C 403 Details of bonding type rmsd hydrogen bonds : bond 0.17369 ( 1166) hydrogen bonds : angle 7.82118 ( 3291) SS BOND : bond 0.00737 ( 49) SS BOND : angle 1.74211 ( 98) covalent geometry : bond 0.01580 (32392) covalent geometry : angle 1.89992 (44169) Misc. bond : bond 0.53490 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 427 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.2895 (OUTLIER) cc_final: 0.2506 (mp) REVERT: B 866 THR cc_start: 0.7407 (p) cc_final: 0.6795 (t) outliers start: 26 outliers final: 2 residues processed: 452 average time/residue: 1.0134 time to fit residues: 572.0582 Evaluate side-chains 207 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 0.1980 chunk 313 optimal weight: 8.9990 chunk 174 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 167 optimal weight: 0.0570 chunk 324 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 0.3980 chunk 241 optimal weight: 0.8980 chunk 375 optimal weight: 20.0000 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 360 ASN A 505 HIS A 751 ASN A 784 GLN A 856 ASN A1010 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 784 GLN B 914 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 49 HIS C 61 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 901 GLN C1002 GLN C1074 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 166 GLN F 24 GLN F 27 GLN F 166 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.234603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.167542 restraints weight = 46365.188| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 5.84 r_work: 0.3392 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32443 Z= 0.153 Angle : 0.633 9.833 44267 Z= 0.338 Chirality : 0.047 0.294 5043 Planarity : 0.005 0.068 5728 Dihedral : 5.071 58.328 4472 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.23 % Rotamer: Outliers : 2.24 % Allowed : 9.02 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.31 (0.13), residues: 4111 helix: 2.57 (0.21), residues: 648 sheet: 0.26 (0.15), residues: 1121 loop : -1.31 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 36 HIS 0.004 0.001 HIS A 207 PHE 0.037 0.002 PHE B 377 TYR 0.023 0.002 TYR B 265 ARG 0.006 0.001 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 1166) hydrogen bonds : angle 5.75889 ( 3291) SS BOND : bond 0.00497 ( 49) SS BOND : angle 1.50037 ( 98) covalent geometry : bond 0.00306 (32392) covalent geometry : angle 0.63010 (44169) Misc. bond : bond 0.00700 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: A 720 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7170 (pp) REVERT: B 190 ARG cc_start: 0.5984 (mtt-85) cc_final: 0.5530 (mtp-110) REVERT: B 191 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6149 (pm20) REVERT: B 314 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 353 TRP cc_start: 0.4606 (p-90) cc_final: 0.4335 (p-90) REVERT: B 916 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7931 (tt) REVERT: B 1006 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8665 (t) REVERT: C 58 PHE cc_start: 0.6495 (m-10) cc_final: 0.5765 (m-10) REVERT: C 142 ASP cc_start: 0.4292 (OUTLIER) cc_final: 0.4059 (p0) REVERT: C 537 LYS cc_start: 0.7457 (mtpt) cc_final: 0.6834 (tttp) REVERT: E 115 VAL cc_start: 0.0897 (OUTLIER) cc_final: 0.0425 (p) REVERT: D 4 MET cc_start: 0.0606 (mpp) cc_final: -0.0510 (mtt) REVERT: D 29 ILE cc_start: 0.3512 (OUTLIER) cc_final: 0.2627 (mm) REVERT: D 104 LEU cc_start: -0.0848 (tt) cc_final: -0.1116 (mm) REVERT: G 115 VAL cc_start: -0.0304 (OUTLIER) cc_final: -0.0601 (p) outliers start: 76 outliers final: 30 residues processed: 274 average time/residue: 1.0519 time to fit residues: 361.4932 Evaluate side-chains 213 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 398 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 406 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 965 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.230504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.175861 restraints weight = 45807.946| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.47 r_work: 0.3368 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 32443 Z= 0.160 Angle : 0.629 14.460 44267 Z= 0.333 Chirality : 0.048 0.244 5043 Planarity : 0.005 0.107 5728 Dihedral : 4.924 59.585 4468 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 3.51 % Allowed : 10.68 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 4111 helix: 2.23 (0.20), residues: 653 sheet: 0.33 (0.15), residues: 1096 loop : -1.34 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 353 HIS 0.006 0.001 HIS A1064 PHE 0.022 0.002 PHE A 906 TYR 0.027 0.002 TYR C 265 ARG 0.008 0.001 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.05907 ( 1166) hydrogen bonds : angle 5.49377 ( 3291) SS BOND : bond 0.00740 ( 49) SS BOND : angle 1.81086 ( 98) covalent geometry : bond 0.00370 (32392) covalent geometry : angle 0.62388 (44169) Misc. bond : bond 0.00404 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 212 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: A 756 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7590 (t80) REVERT: B 64 TRP cc_start: 0.7774 (t60) cc_final: 0.7510 (t60) REVERT: B 190 ARG cc_start: 0.6399 (mtt-85) cc_final: 0.6008 (mtp-110) REVERT: B 191 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6480 (pm20) REVERT: B 269 TYR cc_start: 0.7205 (m-80) cc_final: 0.6878 (m-10) REVERT: C 304 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7637 (mtpm) REVERT: C 512 VAL cc_start: 0.4297 (OUTLIER) cc_final: 0.3964 (m) REVERT: C 537 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7184 (tttp) REVERT: D 4 MET cc_start: 0.0915 (mpp) cc_final: 0.0114 (mtt) REVERT: F 33 LEU cc_start: 0.1622 (OUTLIER) cc_final: 0.1325 (mm) outliers start: 119 outliers final: 42 residues processed: 301 average time/residue: 0.9525 time to fit residues: 368.3313 Evaluate side-chains 196 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 264 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 315 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 404 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 ASN B 196 ASN B 321 GLN B 992 GLN C 755 GLN C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.229688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.170810 restraints weight = 45454.869| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.44 r_work: 0.3300 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32443 Z= 0.117 Angle : 0.552 11.903 44267 Z= 0.289 Chirality : 0.045 0.228 5043 Planarity : 0.004 0.061 5728 Dihedral : 4.630 57.720 4468 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 2.71 % Allowed : 13.27 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.21 (0.13), residues: 4111 helix: 2.68 (0.20), residues: 631 sheet: 0.44 (0.15), residues: 1116 loop : -1.29 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE B 329 TYR 0.022 0.001 TYR B 265 ARG 0.004 0.000 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 1166) hydrogen bonds : angle 5.21072 ( 3291) SS BOND : bond 0.00485 ( 49) SS BOND : angle 1.39039 ( 98) covalent geometry : bond 0.00265 (32392) covalent geometry : angle 0.54904 (44169) Misc. bond : bond 0.00373 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 179 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6782 (ttt-90) REVERT: A 309 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 329 PHE cc_start: 0.6313 (m-80) cc_final: 0.6009 (m-80) REVERT: B 64 TRP cc_start: 0.7657 (t60) cc_final: 0.7357 (t60) REVERT: B 190 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.5657 (mtp-110) REVERT: B 191 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6391 (pm20) REVERT: B 269 TYR cc_start: 0.7185 (m-80) cc_final: 0.6816 (m-10) REVERT: C 320 VAL cc_start: 0.8076 (p) cc_final: 0.7827 (m) REVERT: C 720 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7743 (pp) REVERT: D 4 MET cc_start: 0.0303 (mpp) cc_final: -0.0653 (mtt) outliers start: 92 outliers final: 45 residues processed: 245 average time/residue: 1.0144 time to fit residues: 313.6022 Evaluate side-chains 199 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 27 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 345 optimal weight: 0.0570 chunk 320 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 372 optimal weight: 20.0000 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 784 GLN B 914 ASN B 992 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.227005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.169764 restraints weight = 44470.118| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.34 r_work: 0.3280 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32443 Z= 0.166 Angle : 0.604 12.242 44267 Z= 0.319 Chirality : 0.047 0.222 5043 Planarity : 0.005 0.062 5728 Dihedral : 4.771 54.617 4468 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 3.24 % Allowed : 14.39 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.34 (0.13), residues: 4111 helix: 2.35 (0.21), residues: 633 sheet: 0.32 (0.14), residues: 1142 loop : -1.30 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.032 0.002 PHE B 400 TYR 0.024 0.002 TYR C 265 ARG 0.008 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.06002 ( 1166) hydrogen bonds : angle 5.33307 ( 3291) SS BOND : bond 0.00627 ( 49) SS BOND : angle 1.91586 ( 98) covalent geometry : bond 0.00398 (32392) covalent geometry : angle 0.59778 (44169) Misc. bond : bond 0.00343 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 168 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7959 (m-80) cc_final: 0.7729 (m-80) REVERT: A 309 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: A 740 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8440 (ttt) REVERT: B 54 LEU cc_start: 0.8309 (mt) cc_final: 0.8035 (mp) REVERT: B 64 TRP cc_start: 0.7836 (t60) cc_final: 0.7578 (t60) REVERT: B 172 SER cc_start: 0.6345 (t) cc_final: 0.5986 (t) REVERT: B 190 ARG cc_start: 0.6332 (mtt-85) cc_final: 0.6001 (mtp-110) REVERT: B 191 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6620 (mp0) REVERT: B 269 TYR cc_start: 0.7234 (m-80) cc_final: 0.6920 (m-10) REVERT: B 811 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7304 (pttt) REVERT: B 957 GLN cc_start: 0.8408 (tp40) cc_final: 0.8201 (tt0) REVERT: C 189 LEU cc_start: 0.6647 (mp) cc_final: 0.6177 (tp) REVERT: C 321 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: C 512 VAL cc_start: 0.4390 (OUTLIER) cc_final: 0.4124 (m) REVERT: C 513 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3869 (tp) REVERT: C 720 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.7851 (pt) REVERT: E 34 MET cc_start: 0.2724 (pmm) cc_final: 0.1714 (ttm) REVERT: D 4 MET cc_start: -0.0010 (mpp) cc_final: -0.1142 (mtm) outliers start: 110 outliers final: 60 residues processed: 254 average time/residue: 1.0289 time to fit residues: 331.1545 Evaluate side-chains 206 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 139 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 374 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 chunk 115 optimal weight: 7.9990 chunk 245 optimal weight: 0.3980 chunk 406 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 236 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 overall best weight: 2.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A1010 GLN B 992 GLN C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.225281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.168392 restraints weight = 44415.030| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.46 r_work: 0.3244 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32443 Z= 0.218 Angle : 0.629 13.070 44267 Z= 0.334 Chirality : 0.049 0.222 5043 Planarity : 0.005 0.066 5728 Dihedral : 4.878 41.872 4466 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 3.42 % Allowed : 15.25 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.51 (0.13), residues: 4111 helix: 2.13 (0.20), residues: 634 sheet: 0.17 (0.14), residues: 1159 loop : -1.37 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.006 0.001 HIS C1048 PHE 0.020 0.002 PHE B 559 TYR 0.024 0.002 TYR C 265 ARG 0.013 0.001 ARG B 995 Details of bonding type rmsd hydrogen bonds : bond 0.06469 ( 1166) hydrogen bonds : angle 5.39114 ( 3291) SS BOND : bond 0.00761 ( 49) SS BOND : angle 2.04130 ( 98) covalent geometry : bond 0.00531 (32392) covalent geometry : angle 0.62237 (44169) Misc. bond : bond 0.00396 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 161 time to evaluate : 3.259 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6336 (mtt180) cc_final: 0.5524 (mtm110) REVERT: A 200 TYR cc_start: 0.7981 (m-80) cc_final: 0.7629 (m-80) REVERT: A 309 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: A 740 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8474 (ttt) REVERT: B 64 TRP cc_start: 0.7734 (t60) cc_final: 0.7517 (t60) REVERT: B 190 ARG cc_start: 0.6373 (mtt-85) cc_final: 0.5970 (mtp-110) REVERT: B 191 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6575 (mp0) REVERT: B 239 GLN cc_start: 0.7550 (tp40) cc_final: 0.7081 (tp40) REVERT: B 269 TYR cc_start: 0.7273 (m-80) cc_final: 0.6876 (m-10) REVERT: B 329 PHE cc_start: 0.6184 (m-80) cc_final: 0.5833 (m-80) REVERT: B 588 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7883 (p) REVERT: B 811 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7247 (pttt) REVERT: C 28 TYR cc_start: 0.7268 (m-80) cc_final: 0.6965 (m-80) REVERT: C 189 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6240 (tp) REVERT: C 242 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4031 (tp) REVERT: C 321 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: C 512 VAL cc_start: 0.4368 (OUTLIER) cc_final: 0.4105 (m) REVERT: C 513 LEU cc_start: 0.4333 (OUTLIER) cc_final: 0.3959 (tp) REVERT: C 720 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.7943 (pt) outliers start: 116 outliers final: 67 residues processed: 257 average time/residue: 0.9927 time to fit residues: 323.6388 Evaluate side-chains 217 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 140 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 242 optimal weight: 20.0000 chunk 249 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 302 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 340 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 283 optimal weight: 0.5980 chunk 375 optimal weight: 30.0000 chunk 187 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN B 957 GLN B 992 GLN C 196 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.226977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.171369 restraints weight = 44792.181| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.52 r_work: 0.3290 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32443 Z= 0.113 Angle : 0.552 11.706 44267 Z= 0.288 Chirality : 0.045 0.455 5043 Planarity : 0.004 0.064 5728 Dihedral : 4.504 39.967 4466 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 2.39 % Allowed : 16.78 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.27 (0.13), residues: 4111 helix: 2.40 (0.21), residues: 634 sheet: 0.36 (0.15), residues: 1124 loop : -1.25 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.004 0.001 HIS E 102 PHE 0.013 0.001 PHE C 192 TYR 0.023 0.001 TYR B 265 ARG 0.011 0.000 ARG B 995 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 1166) hydrogen bonds : angle 5.10708 ( 3291) SS BOND : bond 0.00568 ( 49) SS BOND : angle 2.05877 ( 98) covalent geometry : bond 0.00252 (32392) covalent geometry : angle 0.54378 (44169) Misc. bond : bond 0.00302 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 154 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6005 (mtt180) cc_final: 0.5368 (mtm110) REVERT: A 200 TYR cc_start: 0.7922 (m-80) cc_final: 0.7569 (m-80) REVERT: A 309 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: B 64 TRP cc_start: 0.7711 (t60) cc_final: 0.7455 (t60) REVERT: B 190 ARG cc_start: 0.6189 (mtt-85) cc_final: 0.5826 (mtp-110) REVERT: B 191 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6537 (mp0) REVERT: B 269 TYR cc_start: 0.7380 (m-80) cc_final: 0.6984 (m-10) REVERT: B 588 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7796 (p) REVERT: C 28 TYR cc_start: 0.7242 (m-80) cc_final: 0.7011 (m-80) REVERT: C 189 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6615 (tp) REVERT: C 512 VAL cc_start: 0.4413 (OUTLIER) cc_final: 0.4148 (m) REVERT: C 513 LEU cc_start: 0.4284 (OUTLIER) cc_final: 0.3925 (tp) REVERT: C 720 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7829 (pt) REVERT: C 1084 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8230 (t0) REVERT: E 34 MET cc_start: 0.3120 (ppp) cc_final: 0.1770 (ttm) REVERT: D 4 MET cc_start: 0.0411 (OUTLIER) cc_final: -0.0591 (mtt) outliers start: 81 outliers final: 43 residues processed: 216 average time/residue: 0.9978 time to fit residues: 273.8784 Evaluate side-chains 194 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 378 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 388 ASN B 954 HIS B 957 GLN B 992 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 901 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.224165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.165954 restraints weight = 44251.547| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.35 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32443 Z= 0.260 Angle : 0.678 11.305 44267 Z= 0.358 Chirality : 0.050 0.309 5043 Planarity : 0.005 0.064 5728 Dihedral : 4.982 41.820 4466 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 2.80 % Allowed : 16.46 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.60 (0.13), residues: 4111 helix: 1.86 (0.20), residues: 641 sheet: 0.18 (0.15), residues: 1119 loop : -1.40 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 64 HIS 0.007 0.001 HIS C1048 PHE 0.027 0.002 PHE A 32 TYR 0.031 0.002 TYR C 265 ARG 0.007 0.001 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.07161 ( 1166) hydrogen bonds : angle 5.52555 ( 3291) SS BOND : bond 0.00854 ( 49) SS BOND : angle 2.60166 ( 98) covalent geometry : bond 0.00646 (32392) covalent geometry : angle 0.66745 (44169) Misc. bond : bond 0.00445 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 151 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 534 VAL cc_start: 0.7574 (t) cc_final: 0.7172 (m) REVERT: B 64 TRP cc_start: 0.7712 (t60) cc_final: 0.7503 (t60) REVERT: B 190 ARG cc_start: 0.6399 (mtt-85) cc_final: 0.5985 (mtp-110) REVERT: B 191 GLU cc_start: 0.7806 (mt-10) cc_final: 0.6941 (mp0) REVERT: B 239 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7120 (tp40) REVERT: B 269 TYR cc_start: 0.7346 (m-80) cc_final: 0.6885 (m-10) REVERT: B 329 PHE cc_start: 0.6215 (m-80) cc_final: 0.5725 (m-80) REVERT: B 588 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8015 (p) REVERT: B 811 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7114 (ptpt) REVERT: C 189 LEU cc_start: 0.6937 (mp) cc_final: 0.6592 (tp) REVERT: C 512 VAL cc_start: 0.4287 (OUTLIER) cc_final: 0.4004 (m) REVERT: C 513 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.3992 (tp) REVERT: C 720 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8105 (pt) REVERT: C 983 ARG cc_start: 0.7425 (ptm-80) cc_final: 0.6532 (ttp80) REVERT: C 1084 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8327 (t0) REVERT: E 11 LEU cc_start: 0.3308 (mm) cc_final: 0.2822 (mm) REVERT: E 34 MET cc_start: 0.3078 (ppp) cc_final: 0.1852 (ttm) REVERT: H 83 MET cc_start: -0.0297 (OUTLIER) cc_final: -0.1224 (mpp) outliers start: 95 outliers final: 62 residues processed: 228 average time/residue: 1.0277 time to fit residues: 295.6256 Evaluate side-chains 213 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 175 optimal weight: 1.9990 chunk 324 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 195 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS B 957 GLN B 992 GLN C 196 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.225593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169448 restraints weight = 44365.235| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.42 r_work: 0.3267 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32443 Z= 0.135 Angle : 0.570 11.276 44267 Z= 0.299 Chirality : 0.046 0.263 5043 Planarity : 0.005 0.064 5728 Dihedral : 4.617 40.198 4466 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 2.01 % Allowed : 17.37 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.43 (0.13), residues: 4111 helix: 2.19 (0.20), residues: 640 sheet: 0.32 (0.15), residues: 1101 loop : -1.35 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS E 102 PHE 0.013 0.001 PHE C1121 TYR 0.023 0.001 TYR B 265 ARG 0.008 0.000 ARG B 995 Details of bonding type rmsd hydrogen bonds : bond 0.05286 ( 1166) hydrogen bonds : angle 5.23105 ( 3291) SS BOND : bond 0.00548 ( 49) SS BOND : angle 1.86740 ( 98) covalent geometry : bond 0.00316 (32392) covalent geometry : angle 0.56364 (44169) Misc. bond : bond 0.00330 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 148 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6556 (mtt180) cc_final: 0.5642 (mtm110) REVERT: A 309 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 534 VAL cc_start: 0.7542 (t) cc_final: 0.7146 (m) REVERT: B 64 TRP cc_start: 0.7609 (t60) cc_final: 0.7389 (t60) REVERT: B 190 ARG cc_start: 0.6210 (mtt-85) cc_final: 0.5837 (mtp-110) REVERT: B 191 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6668 (mp0) REVERT: B 239 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6918 (tp40) REVERT: B 269 TYR cc_start: 0.7408 (m-80) cc_final: 0.7040 (m-10) REVERT: B 329 PHE cc_start: 0.6135 (m-80) cc_final: 0.5665 (m-80) REVERT: B 588 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 619 GLU cc_start: 0.6360 (pt0) cc_final: 0.5999 (pt0) REVERT: C 189 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6839 (tp) REVERT: C 314 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: C 512 VAL cc_start: 0.4339 (OUTLIER) cc_final: 0.4087 (m) REVERT: C 513 LEU cc_start: 0.4350 (OUTLIER) cc_final: 0.3958 (tp) REVERT: C 720 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7880 (pt) REVERT: C 983 ARG cc_start: 0.7254 (ptm-80) cc_final: 0.6417 (ttp80) REVERT: C 1084 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8319 (t0) REVERT: E 34 MET cc_start: 0.3011 (ppp) cc_final: 0.1736 (ttm) REVERT: D 4 MET cc_start: 0.0263 (mmt) cc_final: -0.0705 (mtt) outliers start: 68 outliers final: 47 residues processed: 199 average time/residue: 1.0909 time to fit residues: 273.2865 Evaluate side-chains 194 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 315 optimal weight: 8.9990 chunk 307 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS B 957 GLN B 992 GLN C 196 ASN C 901 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.224934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168109 restraints weight = 44400.752| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.37 r_work: 0.3249 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32443 Z= 0.164 Angle : 0.591 10.768 44267 Z= 0.310 Chirality : 0.047 0.245 5043 Planarity : 0.005 0.064 5728 Dihedral : 4.622 40.305 4466 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 2.12 % Allowed : 17.43 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.42 (0.13), residues: 4111 helix: 2.21 (0.21), residues: 641 sheet: 0.29 (0.15), residues: 1107 loop : -1.34 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS E 102 PHE 0.016 0.002 PHE C 65 TYR 0.023 0.001 TYR C 265 ARG 0.007 0.000 ARG B 995 Details of bonding type rmsd hydrogen bonds : bond 0.05729 ( 1166) hydrogen bonds : angle 5.23247 ( 3291) SS BOND : bond 0.00573 ( 49) SS BOND : angle 1.97731 ( 98) covalent geometry : bond 0.00394 (32392) covalent geometry : angle 0.58430 (44169) Misc. bond : bond 0.00372 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 146 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6426 (mtt180) cc_final: 0.5782 (mtm110) REVERT: A 309 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 534 VAL cc_start: 0.7594 (t) cc_final: 0.7219 (m) REVERT: B 64 TRP cc_start: 0.7673 (t60) cc_final: 0.7434 (t60) REVERT: B 190 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.6084 (mtp-110) REVERT: B 191 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6826 (mp0) REVERT: B 239 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: B 269 TYR cc_start: 0.7401 (m-80) cc_final: 0.6988 (m-10) REVERT: B 329 PHE cc_start: 0.6398 (m-80) cc_final: 0.5964 (m-80) REVERT: B 588 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7807 (p) REVERT: B 619 GLU cc_start: 0.6490 (pt0) cc_final: 0.6143 (pt0) REVERT: B 995 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8032 (ptm160) REVERT: C 189 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6830 (tp) REVERT: C 314 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: C 512 VAL cc_start: 0.4367 (OUTLIER) cc_final: 0.4085 (m) REVERT: C 513 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.3955 (tp) REVERT: C 619 GLU cc_start: 0.7813 (mp0) cc_final: 0.7433 (tm-30) REVERT: C 720 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.7953 (pt) REVERT: C 983 ARG cc_start: 0.7306 (ptm-80) cc_final: 0.6486 (ttp80) REVERT: E 11 LEU cc_start: 0.3277 (mm) cc_final: 0.2785 (mm) REVERT: E 34 MET cc_start: 0.3176 (ppp) cc_final: 0.1739 (ttm) REVERT: D 4 MET cc_start: 0.0341 (OUTLIER) cc_final: -0.0640 (mtt) REVERT: H 83 MET cc_start: -0.0144 (OUTLIER) cc_final: -0.1221 (mpp) outliers start: 72 outliers final: 51 residues processed: 202 average time/residue: 1.1028 time to fit residues: 276.8522 Evaluate side-chains 196 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 29 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 169 optimal weight: 0.6980 chunk 245 optimal weight: 9.9990 chunk 158 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 992 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.228988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.172466 restraints weight = 46667.738| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.08 r_work: 0.3601 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32443 Z= 0.111 Angle : 0.551 11.107 44267 Z= 0.286 Chirality : 0.044 0.219 5043 Planarity : 0.004 0.064 5728 Dihedral : 4.414 38.341 4466 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 1.77 % Allowed : 17.66 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.27 (0.13), residues: 4111 helix: 2.49 (0.21), residues: 635 sheet: 0.37 (0.15), residues: 1099 loop : -1.27 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS E 102 PHE 0.013 0.001 PHE C 377 TYR 0.023 0.001 TYR B 265 ARG 0.008 0.000 ARG B 995 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 1166) hydrogen bonds : angle 5.06072 ( 3291) SS BOND : bond 0.00463 ( 49) SS BOND : angle 1.72450 ( 98) covalent geometry : bond 0.00250 (32392) covalent geometry : angle 0.54512 (44169) Misc. bond : bond 0.00320 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26849.31 seconds wall clock time: 462 minutes 16.09 seconds (27736.09 seconds total)