Starting phenix.real_space_refine on Mon Aug 25 23:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yww_39645/08_2025/8yww_39645_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yww_39645/08_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_39645/08_2025/8yww_39645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yww_39645/08_2025/8yww_39645.map" model { file = "/net/cci-nas-00/data/ceres_data/8yww_39645/08_2025/8yww_39645_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yww_39645/08_2025/8yww_39645_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 6, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} 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: {'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 6, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} 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: {'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 6, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} 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: 6.19, per 1000 atoms: 0.20 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.57 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: 8.08 Time building geometry restraints manager: 2.77 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: 4.840 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: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.210 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.810 ------------------------------------------------------------------------------- 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 : 15.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG C 403 TYR 0.029 0.002 TYR B 453 PHE 0.020 0.002 PHE B 400 TRP 0.044 0.002 TRP B 353 HIS 0.006 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.01580 (32392) covalent geometry : angle 1.89992 (44169) SS BOND : bond 0.00737 ( 49) SS BOND : angle 1.74211 ( 98) hydrogen bonds : bond 0.17369 ( 1166) hydrogen bonds : angle 7.82118 ( 3291) 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 : 0.791 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: 0.2504 (mp) REVERT: B 866 THR cc_start: 0.7407 (p) cc_final: 0.6796 (t) outliers start: 26 outliers final: 2 residues processed: 452 average time/residue: 0.4506 time to fit residues: 253.4143 Evaluate side-chains 205 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.3980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0030 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 A1010 GLN B 125 ASN B 196 ASN 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 755 GLN C 901 GLN C1074 ASN E 32 ASN D 27 GLN D 166 GLN F 24 GLN F 27 GLN F 166 GLN G 32 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.231932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.166633 restraints weight = 46043.518| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 5.84 r_work: 0.3330 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32443 Z= 0.193 Angle : 0.681 10.850 44267 Z= 0.363 Chirality : 0.049 0.271 5043 Planarity : 0.006 0.066 5728 Dihedral : 5.220 58.794 4472 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.70 % Rotamer: Outliers : 2.45 % Allowed : 9.55 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.13), residues: 4111 helix: 2.32 (0.20), residues: 652 sheet: 0.22 (0.15), residues: 1097 loop : -1.37 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 457 TYR 0.026 0.002 TYR B 265 PHE 0.033 0.002 PHE B 377 TRP 0.028 0.001 TRP H 36 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00406 (32392) covalent geometry : angle 0.67737 (44169) SS BOND : bond 0.00483 ( 49) SS BOND : angle 1.64147 ( 98) hydrogen bonds : bond 0.05568 ( 1166) hydrogen bonds : angle 5.78854 ( 3291) Misc. bond : bond 0.02107 ( 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 295 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 212 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: A 532 ASN cc_start: 0.7775 (t0) cc_final: 0.7524 (t0) REVERT: A 567 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8213 (ttp-170) REVERT: A 720 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7500 (pt) REVERT: B 54 LEU cc_start: 0.7810 (mt) cc_final: 0.7418 (mp) REVERT: B 64 TRP cc_start: 0.7574 (t60) cc_final: 0.7229 (t60) REVERT: B 190 ARG cc_start: 0.6064 (mtt-85) cc_final: 0.5629 (mtp-110) REVERT: B 191 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6063 (pm20) REVERT: B 226 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5594 (mt) REVERT: B 488 CYS cc_start: 0.2402 (OUTLIER) cc_final: 0.1905 (p) REVERT: C 58 PHE cc_start: 0.7194 (m-10) cc_final: 0.6936 (m-10) REVERT: C 142 ASP cc_start: 0.4592 (OUTLIER) cc_final: 0.4384 (p0) REVERT: C 537 LYS cc_start: 0.7628 (mtpt) cc_final: 0.6996 (tttp) REVERT: E 115 VAL cc_start: 0.0960 (OUTLIER) cc_final: 0.0498 (p) REVERT: D 4 MET cc_start: 0.0489 (mpp) cc_final: -0.0613 (mtt) REVERT: D 29 ILE cc_start: 0.3674 (OUTLIER) cc_final: 0.2781 (mm) REVERT: D 104 LEU cc_start: -0.0820 (tt) cc_final: -0.1092 (mm) REVERT: G 115 VAL cc_start: -0.0051 (OUTLIER) cc_final: -0.0285 (p) outliers start: 83 outliers final: 29 residues processed: 274 average time/residue: 0.5019 time to fit residues: 171.9018 Evaluate side-chains 212 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG 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 761 THR 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 B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU 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 735 SER 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 131 CYS 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 705 VAL Chi-restraints excluded: chain C residue 964 LYS 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 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 273 optimal weight: 0.0370 chunk 389 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 85 optimal weight: 0.0020 chunk 352 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 856 ASN B 207 HIS B 992 GLN C 751 ASN C 755 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.229222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.173901 restraints weight = 45038.697| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.50 r_work: 0.3313 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32443 Z= 0.171 Angle : 0.626 10.208 44267 Z= 0.332 Chirality : 0.048 0.244 5043 Planarity : 0.005 0.085 5728 Dihedral : 4.955 58.400 4468 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 3.66 % Allowed : 11.29 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.13), residues: 4111 helix: 2.23 (0.21), residues: 648 sheet: 0.30 (0.15), residues: 1122 loop : -1.41 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 71 TYR 0.025 0.002 TYR B 265 PHE 0.028 0.002 PHE G 67 TRP 0.026 0.002 TRP B 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00399 (32392) covalent geometry : angle 0.62177 (44169) SS BOND : bond 0.00909 ( 49) SS BOND : angle 1.59885 ( 98) hydrogen bonds : bond 0.06019 ( 1166) hydrogen bonds : angle 5.54985 ( 3291) Misc. bond : bond 0.00601 ( 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 338 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 214 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: A 756 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7633 (t80) REVERT: A 975 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 54 LEU cc_start: 0.8108 (mt) cc_final: 0.7796 (mp) REVERT: B 64 TRP cc_start: 0.7784 (t60) cc_final: 0.7536 (t60) REVERT: B 190 ARG cc_start: 0.6323 (mtt-85) cc_final: 0.5987 (mtp-110) REVERT: B 191 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6550 (pm20) REVERT: B 269 TYR cc_start: 0.7261 (m-80) cc_final: 0.6953 (m-10) REVERT: B 314 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8672 (tm-30) REVERT: B 329 PHE cc_start: 0.5528 (m-80) cc_final: 0.5146 (m-80) REVERT: C 58 PHE cc_start: 0.8425 (m-10) cc_final: 0.8157 (m-10) REVERT: C 129 LYS cc_start: 0.6505 (mtpt) cc_final: 0.6079 (pptt) REVERT: C 142 ASP cc_start: 0.4474 (OUTLIER) cc_final: 0.4222 (p0) REVERT: C 287 ASP cc_start: 0.7118 (t0) cc_final: 0.6859 (m-30) REVERT: C 512 VAL cc_start: 0.4372 (OUTLIER) cc_final: 0.4046 (m) REVERT: C 537 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7149 (tttp) REVERT: C 705 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8249 (t) REVERT: C 955 ASN cc_start: 0.7797 (m110) cc_final: 0.7573 (m-40) REVERT: D 4 MET cc_start: 0.0521 (mpp) cc_final: -0.0267 (mtt) REVERT: D 27 GLN cc_start: 0.3173 (OUTLIER) cc_final: 0.2914 (pm20) REVERT: D 199 GLN cc_start: 0.1118 (mt0) cc_final: 0.0839 (tp40) REVERT: F 33 LEU cc_start: 0.1937 (OUTLIER) cc_final: 0.1705 (mm) outliers start: 124 outliers final: 46 residues processed: 302 average time/residue: 0.4333 time to fit residues: 166.1537 Evaluate side-chains 212 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 208 THR 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 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 878 LEU 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 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 314 GLN 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 752 LEU 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 131 CYS Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 GLU 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 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE 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 D residue 27 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 278 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 319 optimal weight: 40.0000 chunk 391 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 314 GLN B 321 GLN B 949 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN F 124 GLN G 201 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.226596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.169924 restraints weight = 44433.353| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.33 r_work: 0.3263 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32443 Z= 0.193 Angle : 0.628 13.952 44267 Z= 0.331 Chirality : 0.048 0.226 5043 Planarity : 0.005 0.064 5728 Dihedral : 4.993 54.908 4468 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 3.66 % Allowed : 13.21 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.13), residues: 4111 helix: 2.15 (0.21), residues: 642 sheet: 0.25 (0.14), residues: 1136 loop : -1.43 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 983 TYR 0.024 0.002 TYR C 265 PHE 0.018 0.002 PHE A 32 TRP 0.018 0.002 TRP A 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00465 (32392) covalent geometry : angle 0.62185 (44169) SS BOND : bond 0.00606 ( 49) SS BOND : angle 1.90312 ( 98) hydrogen bonds : bond 0.06234 ( 1166) hydrogen bonds : angle 5.48204 ( 3291) Misc. bond : bond 0.00404 ( 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 304 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 180 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: B 32 PHE cc_start: 0.6671 (m-80) cc_final: 0.6299 (m-80) REVERT: B 54 LEU cc_start: 0.8241 (mt) cc_final: 0.7982 (mp) REVERT: B 64 TRP cc_start: 0.7803 (t60) cc_final: 0.7558 (t60) REVERT: B 190 ARG cc_start: 0.6238 (mtt-85) cc_final: 0.5977 (mtp-110) REVERT: B 191 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6467 (mp0) REVERT: B 269 TYR cc_start: 0.7223 (m-80) cc_final: 0.6887 (m-10) REVERT: B 957 GLN cc_start: 0.8420 (tp40) cc_final: 0.8190 (tt0) REVERT: C 271 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: C 304 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7984 (mtpm) REVERT: C 314 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: C 513 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3991 (tp) REVERT: C 705 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8565 (t) REVERT: C 720 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.7971 (pt) REVERT: E 112 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4674 (mt) REVERT: D 4 MET cc_start: -0.0146 (mpp) cc_final: -0.1265 (mtt) REVERT: D 199 GLN cc_start: 0.1560 (mt0) cc_final: 0.0855 (tp40) outliers start: 124 outliers final: 64 residues processed: 280 average time/residue: 0.4896 time to fit residues: 172.8497 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 : 1.074 ------------------------------------------------------------------------------- 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 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 761 THR Chi-restraints excluded: chain A residue 791 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 996 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 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 525 CYS 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 826 VAL 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 B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL 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 271 GLN Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 314 GLN 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 705 VAL 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 963 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 18 LEU 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 E residue 176 SER Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 120 THR 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 161 optimal weight: 3.9990 chunk 391 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 282 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 376 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 207 HIS B 314 GLN B 949 GLN B 992 GLN C 901 GLN ** C 992 GLN ** 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 = 0.226976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161037 restraints weight = 44787.258| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 5.77 r_work: 0.3160 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32443 Z= 0.121 Angle : 0.561 13.532 44267 Z= 0.294 Chirality : 0.045 0.224 5043 Planarity : 0.004 0.064 5728 Dihedral : 4.609 42.442 4466 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.10 % Allowed : 14.95 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.13), residues: 4111 helix: 2.49 (0.21), residues: 634 sheet: 0.40 (0.15), residues: 1116 loop : -1.32 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.023 0.001 TYR B 265 PHE 0.012 0.001 PHE C1121 TRP 0.040 0.001 TRP B 353 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00276 (32392) covalent geometry : angle 0.55253 (44169) SS BOND : bond 0.00517 ( 49) SS BOND : angle 2.10208 ( 98) hydrogen bonds : bond 0.05012 ( 1166) hydrogen bonds : angle 5.22084 ( 3291) Misc. bond : bond 0.00355 ( 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 265 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 160 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6957 (mp) REVERT: A 309 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 740 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8300 (ttt) REVERT: B 54 LEU cc_start: 0.8008 (mt) cc_final: 0.7792 (mp) REVERT: B 64 TRP cc_start: 0.7562 (t60) cc_final: 0.7281 (t60) REVERT: B 190 ARG cc_start: 0.5721 (mtt-85) cc_final: 0.5384 (mtp-110) REVERT: B 191 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6063 (mp0) REVERT: B 269 TYR cc_start: 0.7120 (m-80) cc_final: 0.6695 (m-10) REVERT: B 329 PHE cc_start: 0.5456 (m-80) cc_final: 0.5142 (m-80) REVERT: B 574 ASP cc_start: 0.7786 (m-30) cc_final: 0.7540 (m-30) REVERT: B 811 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7169 (ptpt) REVERT: B 957 GLN cc_start: 0.8334 (tp40) cc_final: 0.7940 (tt0) REVERT: C 189 LEU cc_start: 0.6217 (mp) cc_final: 0.5847 (tp) REVERT: C 271 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: C 720 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.7890 (pt) REVERT: D 4 MET cc_start: 0.0362 (mpp) cc_final: -0.0716 (mtt) REVERT: D 199 GLN cc_start: 0.2351 (mt0) cc_final: 0.1389 (tp40) REVERT: F 4 MET cc_start: 0.0831 (mmt) cc_final: 0.0604 (mmp) REVERT: G 92 ILE cc_start: 0.2779 (OUTLIER) cc_final: 0.2563 (tp) REVERT: G 115 VAL cc_start: -0.0049 (OUTLIER) cc_final: -0.0279 (p) outliers start: 105 outliers final: 50 residues processed: 247 average time/residue: 0.4923 time to fit residues: 152.2804 Evaluate side-chains 205 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 197 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 318 PHE 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 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 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 208 THR 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 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP 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 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU 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 E residue 18 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 301 optimal weight: 0.0770 chunk 44 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 422 ASN B 314 GLN B 505 HIS B 914 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.223138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156839 restraints weight = 44093.660| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 5.76 r_work: 0.3099 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 32443 Z= 0.346 Angle : 0.755 11.888 44267 Z= 0.400 Chirality : 0.054 0.272 5043 Planarity : 0.006 0.082 5728 Dihedral : 5.359 45.495 4466 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 4.10 % Allowed : 14.45 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.12), residues: 4111 helix: 1.57 (0.20), residues: 638 sheet: 0.06 (0.15), residues: 1123 loop : -1.51 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 31 TYR 0.035 0.003 TYR C 265 PHE 0.024 0.003 PHE A 898 TRP 0.032 0.002 TRP B 353 HIS 0.014 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00853 (32392) covalent geometry : angle 0.74466 (44169) SS BOND : bond 0.00957 ( 49) SS BOND : angle 2.77543 ( 98) hydrogen bonds : bond 0.08128 ( 1166) hydrogen bonds : angle 5.75483 ( 3291) Misc. bond : bond 0.00554 ( 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 294 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 155 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6497 (mtt180) cc_final: 0.5844 (mtm110) REVERT: A 305 SER cc_start: 0.9093 (t) cc_final: 0.8849 (p) REVERT: A 309 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: A 534 VAL cc_start: 0.7610 (t) cc_final: 0.7146 (m) REVERT: B 64 TRP cc_start: 0.7709 (t60) cc_final: 0.7458 (t60) REVERT: B 190 ARG cc_start: 0.6351 (mtt-85) cc_final: 0.5869 (mtp-110) REVERT: B 191 GLU cc_start: 0.7881 (mt-10) cc_final: 0.6911 (mp0) REVERT: B 239 GLN cc_start: 0.7783 (tp40) cc_final: 0.7267 (tp40) REVERT: B 269 TYR cc_start: 0.7513 (m-80) cc_final: 0.7075 (m-10) REVERT: B 588 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 811 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7016 (ptpt) REVERT: C 189 LEU cc_start: 0.6596 (mp) cc_final: 0.6145 (tp) REVERT: C 309 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: C 314 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: C 321 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: C 720 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8292 (pt) REVERT: D 4 MET cc_start: 0.0889 (mpp) cc_final: 0.0103 (ttt) REVERT: F 4 MET cc_start: 0.0831 (mmt) cc_final: 0.0621 (mmp) REVERT: G 92 ILE cc_start: 0.3256 (OUTLIER) cc_final: 0.3029 (tp) REVERT: G 115 VAL cc_start: -0.0009 (OUTLIER) cc_final: -0.0248 (p) outliers start: 139 outliers final: 79 residues processed: 267 average time/residue: 0.5030 time to fit residues: 170.3955 Evaluate side-chains 224 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 136 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 197 ILE 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 318 PHE Chi-restraints excluded: chain A residue 531 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 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 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 A residue 1133 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 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR 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 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL 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 271 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 321 GLN 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 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 964 LYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain G residue 92 ILE 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 40 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 394 optimal weight: 2.9990 chunk 408 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 207 HIS B 314 GLN B 784 GLN B 949 GLN B 954 HIS B 992 GLN C 196 ASN F 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.225959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170144 restraints weight = 44360.713| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.36 r_work: 0.3259 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32443 Z= 0.126 Angle : 0.569 10.014 44267 Z= 0.300 Chirality : 0.045 0.285 5043 Planarity : 0.005 0.066 5728 Dihedral : 4.776 43.870 4466 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.54 % Allowed : 16.66 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.13), residues: 4111 helix: 2.11 (0.21), residues: 638 sheet: 0.17 (0.15), residues: 1119 loop : -1.38 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 995 TYR 0.025 0.001 TYR B 265 PHE 0.015 0.001 PHE C1121 TRP 0.027 0.001 TRP B 353 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00291 (32392) covalent geometry : angle 0.56217 (44169) SS BOND : bond 0.00577 ( 49) SS BOND : angle 1.94281 ( 98) hydrogen bonds : bond 0.05325 ( 1166) hydrogen bonds : angle 5.32515 ( 3291) Misc. bond : bond 0.00358 ( 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 234 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 148 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6271 (mtt180) cc_final: 0.5616 (mtm110) REVERT: A 309 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: A 534 VAL cc_start: 0.7589 (t) cc_final: 0.7192 (m) REVERT: B 64 TRP cc_start: 0.7663 (t60) cc_final: 0.7450 (t60) REVERT: B 190 ARG cc_start: 0.6187 (mtt-85) cc_final: 0.5818 (mtp-110) REVERT: B 191 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7223 (mt-10) REVERT: B 269 TYR cc_start: 0.7465 (m-80) cc_final: 0.7048 (m-10) REVERT: B 329 PHE cc_start: 0.6403 (m-80) cc_final: 0.5910 (m-80) REVERT: B 588 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7894 (p) REVERT: B 811 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7181 (pttt) REVERT: C 189 LEU cc_start: 0.7202 (mp) cc_final: 0.6771 (tp) REVERT: C 309 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: C 398 ASP cc_start: 0.2750 (OUTLIER) cc_final: 0.2176 (t70) REVERT: C 720 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7846 (pt) outliers start: 86 outliers final: 50 residues processed: 217 average time/residue: 0.5370 time to fit residues: 146.4314 Evaluate side-chains 191 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 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 378 LYS 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 705 VAL Chi-restraints excluded: chain A residue 791 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 976 VAL 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 1133 VAL Chi-restraints excluded: chain B residue 208 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 320 VAL Chi-restraints excluded: chain B residue 524 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 811 LYS 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 B residue 1043 CYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 398 ASP 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 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 G residue 111 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 23 VAL 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 133 optimal weight: 0.0370 chunk 132 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 362 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 267 optimal weight: 0.0010 chunk 63 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 overall best weight: 0.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 314 GLN B 784 GLN B 992 GLN C 196 ASN C 417 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.227445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159282 restraints weight = 44592.940| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 5.13 r_work: 0.3230 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32443 Z= 0.102 Angle : 0.527 8.560 44267 Z= 0.277 Chirality : 0.044 0.402 5043 Planarity : 0.004 0.064 5728 Dihedral : 4.381 40.270 4466 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 2.06 % Allowed : 17.28 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.13), residues: 4111 helix: 2.59 (0.21), residues: 635 sheet: 0.41 (0.15), residues: 1119 loop : -1.30 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.023 0.001 TYR B 265 PHE 0.013 0.001 PHE C 377 TRP 0.019 0.001 TRP B 353 HIS 0.003 0.000 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00223 (32392) covalent geometry : angle 0.52272 (44169) SS BOND : bond 0.00482 ( 49) SS BOND : angle 1.57697 ( 98) hydrogen bonds : bond 0.04215 ( 1166) hydrogen bonds : angle 4.98591 ( 3291) Misc. bond : bond 0.00340 ( 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 223 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: A 534 VAL cc_start: 0.7379 (t) cc_final: 0.6981 (m) REVERT: A 740 MET cc_start: 0.8565 (ttt) cc_final: 0.8347 (ttp) REVERT: B 64 TRP cc_start: 0.7535 (t60) cc_final: 0.7225 (t60) REVERT: B 190 ARG cc_start: 0.5847 (mtt-85) cc_final: 0.5421 (mtp-110) REVERT: B 191 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 239 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6954 (tp40) REVERT: B 269 TYR cc_start: 0.7520 (m-80) cc_final: 0.7126 (m-10) REVERT: B 329 PHE cc_start: 0.6022 (m-80) cc_final: 0.5643 (m-80) REVERT: B 588 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 811 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6806 (ptpt) REVERT: C 189 LEU cc_start: 0.7054 (mp) cc_final: 0.6744 (tp) REVERT: C 271 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: C 398 ASP cc_start: 0.2543 (OUTLIER) cc_final: 0.1993 (t70) REVERT: C 720 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7882 (pt) REVERT: C 957 GLN cc_start: 0.8298 (pt0) cc_final: 0.8000 (tt0) REVERT: E 11 LEU cc_start: 0.4105 (mp) cc_final: 0.3882 (mm) REVERT: D 4 MET cc_start: 0.1063 (mpp) cc_final: 0.0126 (ttm) outliers start: 70 outliers final: 40 residues processed: 205 average time/residue: 0.5173 time to fit residues: 131.9573 Evaluate side-chains 188 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 197 ILE 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 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR 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 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 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 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 902 MET Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 398 ASP 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 960 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 339 optimal weight: 9.9990 chunk 323 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 230 optimal weight: 5.9990 chunk 297 optimal weight: 0.0770 chunk 294 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1010 GLN B 207 HIS B 314 GLN B 388 ASN B 784 GLN B 949 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.226133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.168533 restraints weight = 44217.134| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.52 r_work: 0.3261 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32443 Z= 0.125 Angle : 0.546 10.089 44267 Z= 0.285 Chirality : 0.045 0.233 5043 Planarity : 0.004 0.063 5728 Dihedral : 4.393 39.280 4466 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 2.03 % Allowed : 17.40 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.13), residues: 4111 helix: 2.56 (0.21), residues: 638 sheet: 0.41 (0.15), residues: 1113 loop : -1.28 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.023 0.001 TYR B 265 PHE 0.014 0.001 PHE C1121 TRP 0.018 0.001 TRP B 353 HIS 0.003 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00292 (32392) covalent geometry : angle 0.54064 (44169) SS BOND : bond 0.00501 ( 49) SS BOND : angle 1.65117 ( 98) hydrogen bonds : bond 0.04837 ( 1166) hydrogen bonds : angle 5.03728 ( 3291) Misc. bond : bond 0.00365 ( 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 210 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 141 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 534 VAL cc_start: 0.7453 (t) cc_final: 0.7057 (m) REVERT: B 190 ARG cc_start: 0.6313 (mtt-85) cc_final: 0.5992 (mtp-110) REVERT: B 191 GLU cc_start: 0.7812 (mt-10) cc_final: 0.6803 (mp0) REVERT: B 239 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6947 (tp40) REVERT: B 269 TYR cc_start: 0.7388 (m-80) cc_final: 0.6989 (m-10) REVERT: B 329 PHE cc_start: 0.6277 (m-80) cc_final: 0.5707 (m-80) REVERT: B 588 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 811 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.7005 (pttt) REVERT: C 189 LEU cc_start: 0.7164 (mp) cc_final: 0.6898 (tp) REVERT: C 271 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: C 398 ASP cc_start: 0.2778 (OUTLIER) cc_final: 0.2326 (t70) REVERT: C 720 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7842 (pt) REVERT: E 11 LEU cc_start: 0.3957 (mp) cc_final: 0.3681 (mm) REVERT: D 4 MET cc_start: 0.0884 (mpp) cc_final: 0.0121 (ttm) outliers start: 69 outliers final: 51 residues processed: 194 average time/residue: 0.4280 time to fit residues: 104.9944 Evaluate side-chains 194 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 197 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 318 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 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 984 LEU 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 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 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU 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 902 MET Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 398 ASP 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 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain G residue 111 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 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 219 optimal weight: 0.4980 chunk 260 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 232 optimal weight: 0.0030 chunk 84 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 chunk 130 optimal weight: 0.0370 chunk 187 optimal weight: 0.0670 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 949 GLN B 992 GLN C 196 ASN ** C 762 GLN ** 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 = 0.4674 r_free = 0.4674 target = 0.228170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170989 restraints weight = 44553.486| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.29 r_work: 0.3328 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 32443 Z= 0.095 Angle : 0.518 11.669 44267 Z= 0.268 Chirality : 0.044 0.210 5043 Planarity : 0.004 0.062 5728 Dihedral : 4.164 35.691 4466 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 1.77 % Allowed : 17.81 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.13), residues: 4111 helix: 2.70 (0.21), residues: 638 sheet: 0.57 (0.15), residues: 1111 loop : -1.19 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.022 0.001 TYR B 265 PHE 0.014 0.001 PHE C 377 TRP 0.016 0.001 TRP B 353 HIS 0.003 0.000 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00205 (32392) covalent geometry : angle 0.51485 (44169) SS BOND : bond 0.00421 ( 49) SS BOND : angle 1.37509 ( 98) hydrogen bonds : bond 0.03786 ( 1166) hydrogen bonds : angle 4.82305 ( 3291) Misc. bond : bond 0.00338 ( 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 209 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6025 (mtt180) cc_final: 0.5249 (mtm110) REVERT: A 534 VAL cc_start: 0.7174 (t) cc_final: 0.6905 (m) REVERT: A 825 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8226 (mmtt) REVERT: B 190 ARG cc_start: 0.6211 (mtt-85) cc_final: 0.5829 (mtp-110) REVERT: B 191 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6736 (mp0) REVERT: B 239 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6587 (tp40) REVERT: B 269 TYR cc_start: 0.7317 (m-80) cc_final: 0.6957 (m-10) REVERT: B 329 PHE cc_start: 0.6129 (m-80) cc_final: 0.5797 (m-80) REVERT: B 588 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 619 GLU cc_start: 0.6343 (pt0) cc_final: 0.6011 (pt0) REVERT: C 189 LEU cc_start: 0.7385 (mp) cc_final: 0.7068 (tp) REVERT: C 190 ARG cc_start: 0.6992 (mtt-85) cc_final: 0.6754 (mtp180) REVERT: C 398 ASP cc_start: 0.2828 (OUTLIER) cc_final: 0.2331 (t70) REVERT: C 720 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7621 (pt) REVERT: E 11 LEU cc_start: 0.4142 (mp) cc_final: 0.3869 (mm) REVERT: D 4 MET cc_start: 0.0201 (mpp) cc_final: -0.0760 (mtm) outliers start: 60 outliers final: 36 residues processed: 196 average time/residue: 0.4759 time to fit residues: 117.3546 Evaluate side-chains 175 residues out of total 3613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 825 LYS 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 B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL 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 B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 398 ASP 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 E residue 92 ILE 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 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 285 optimal weight: 2.9990 chunk 400 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 348 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 304 optimal weight: 0.0670 chunk 164 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 992 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.227497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162557 restraints weight = 45007.901| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 5.17 r_work: 0.3208 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.315 32443 Z= 0.186 Angle : 0.662 65.900 44267 Z= 0.363 Chirality : 0.044 0.570 5043 Planarity : 0.005 0.115 5728 Dihedral : 4.165 35.682 4466 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 1.33 % Allowed : 18.20 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.13), residues: 4111 helix: 2.71 (0.21), residues: 638 sheet: 0.58 (0.15), residues: 1111 loop : -1.18 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 995 TYR 0.021 0.001 TYR B 265 PHE 0.014 0.001 PHE C 377 TRP 0.015 0.001 TRP B 353 HIS 0.003 0.000 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00391 (32392) covalent geometry : angle 0.65839 (44169) SS BOND : bond 0.00629 ( 49) SS BOND : angle 1.68867 ( 98) hydrogen bonds : bond 0.03830 ( 1166) hydrogen bonds : angle 4.82454 ( 3291) Misc. bond : bond 0.00382 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14915.98 seconds wall clock time: 253 minutes 45.34 seconds (15225.34 seconds total)