Starting phenix.real_space_refine on Tue Sep 15 21:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.cif" model { file = "/net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gen_4396/09_2026/6gen_4396.map" } resolution = 3.6 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 362 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26898 2.51 5 N 7881 2.21 5 O 9204 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44481 Number of models: 1 Model: "" Number of chains: 29 Chain: "Z" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 655 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 130} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 131 Planarities with less than four sites: {'UNK:plan-1': 131} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3525 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "J" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3568 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 7, 'ASP:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23819 SG CYS S 244 49.911 70.845 117.679 1.00 74.04 S ATOM 23839 SG CYS S 247 46.584 68.555 114.591 1.00 61.50 S ATOM 23955 SG CYS S 264 47.615 71.995 114.554 1.00 90.14 S ATOM 23980 SG CYS S 268 45.500 71.489 117.455 1.00 85.21 S ATOM 23899 SG CYS S 256 52.142 78.661 124.394 1.00 96.12 S ATOM 23920 SG CYS S 259 53.977 75.901 126.523 1.00 80.86 S ATOM 24059 SG CYS S 277 50.955 77.008 128.993 1.00111.59 S Time building chain proxies: 10.03, per 1000 atoms: 0.23 Number of scatterers: 44481 At special positions: 0 Unit cell: (169.83, 199.8, 206.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 118 16.00 P 362 15.00 Mg 8 11.99 F 6 9.00 O 9204 8.00 N 7881 7.00 C 26898 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.78 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " Number of angles added : 9 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 44 sheets defined 49.7% alpha, 14.5% beta 167 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 6.37 Creating SS restraints... Processing helix chain 'Z' and resid 101 through 129 removed outlier: 3.562A pdb=" N UNK Z 129 " --> pdb=" O UNK Z 125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 142 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.703A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.704A pdb=" N PHE B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 114 Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.899A pdb=" N ILE C 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.518A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.548A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.899A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.517A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.548A pdb=" N VAL D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 4.249A pdb=" N LYS E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 22' Processing helix chain 'E' and resid 27 through 37 removed outlier: 3.899A pdb=" N VAL E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 74 removed outlier: 3.851A pdb=" N ASN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.556A pdb=" N LEU E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.544A pdb=" N ALA F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'F' and resid 27 through 37 removed outlier: 3.900A pdb=" N VAL F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 74 removed outlier: 3.851A pdb=" N ASN F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.556A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 58 through 87 removed outlier: 3.636A pdb=" N GLU G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.558A pdb=" N ILE G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 126 Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.636A pdb=" N GLU H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.556A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'M' and resid 697 through 712 removed outlier: 4.083A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN M 712 " --> pdb=" O ALA M 708 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 removed outlier: 3.623A pdb=" N GLN M 730 " --> pdb=" O GLY M 726 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 742 " --> pdb=" O LEU M 738 " (cutoff:3.500A) Processing helix chain 'M' and resid 756 through 767 removed outlier: 3.741A pdb=" N TRP M 760 " --> pdb=" O VAL M 756 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 781 through 787 Processing helix chain 'M' and resid 804 through 809 removed outlier: 4.040A pdb=" N GLN M 808 " --> pdb=" O GLN M 804 " (cutoff:3.500A) Processing helix chain 'M' and resid 809 through 814 Processing helix chain 'M' and resid 834 through 840 removed outlier: 4.112A pdb=" N GLN M 838 " --> pdb=" O SER M 834 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 871 removed outlier: 4.087A pdb=" N LEU M 863 " --> pdb=" O ASN M 859 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET M 871 " --> pdb=" O LEU M 867 " (cutoff:3.500A) Processing helix chain 'M' and resid 914 through 925 removed outlier: 3.853A pdb=" N HIS M 922 " --> pdb=" O VAL M 918 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN M 923 " --> pdb=" O ALA M 919 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL M 924 " --> pdb=" O LYS M 920 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 925 " --> pdb=" O LEU M 921 " (cutoff:3.500A) Processing helix chain 'M' and resid 954 through 971 removed outlier: 3.549A pdb=" N LYS M 971 " --> pdb=" O ARG M 967 " (cutoff:3.500A) Processing helix chain 'M' and resid 972 through 975 removed outlier: 4.024A pdb=" N ALA M 975 " --> pdb=" O ALA M 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 972 through 975' Processing helix chain 'M' and resid 979 through 994 removed outlier: 3.729A pdb=" N VAL M 983 " --> pdb=" O PHE M 979 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN M 994 " --> pdb=" O ARG M 990 " (cutoff:3.500A) Processing helix chain 'M' and resid 1013 through 1018 removed outlier: 3.852A pdb=" N ASP M1017 " --> pdb=" O CYS M1013 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1013 through 1018' Processing helix chain 'M' and resid 1018 through 1029 Processing helix chain 'M' and resid 1046 through 1050 Processing helix chain 'M' and resid 1055 through 1064 Processing helix chain 'M' and resid 1070 through 1094 removed outlier: 3.602A pdb=" N LEU M1078 " --> pdb=" O GLU M1074 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M1085 " --> pdb=" O THR M1081 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE M1094 " --> pdb=" O GLY M1090 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1133 removed outlier: 3.695A pdb=" N ASN M1108 " --> pdb=" O PHE M1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP M1117 " --> pdb=" O GLU M1113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET M1118 " --> pdb=" O GLY M1114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M1122 " --> pdb=" O MET M1118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS M1123 " --> pdb=" O LEU M1119 " (cutoff:3.500A) Processing helix chain 'M' and resid 1141 through 1147 removed outlier: 3.808A pdb=" N ASP M1147 " --> pdb=" O LEU M1143 " (cutoff:3.500A) Processing helix chain 'M' and resid 1158 through 1163 removed outlier: 3.530A pdb=" N ILE M1163 " --> pdb=" O ASP M1159 " (cutoff:3.500A) Processing helix chain 'M' and resid 1165 through 1173 removed outlier: 3.738A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1173 through 1181 Processing helix chain 'M' and resid 1192 through 1198 removed outlier: 4.061A pdb=" N LEU M1197 " --> pdb=" O ARG M1193 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY M1198 " --> pdb=" O LYS M1194 " (cutoff:3.500A) Processing helix chain 'M' and resid 1208 through 1220 Processing helix chain 'M' and resid 1224 through 1233 removed outlier: 3.729A pdb=" N ILE M1233 " --> pdb=" O THR M1229 " (cutoff:3.500A) Processing helix chain 'M' and resid 1239 through 1244 removed outlier: 4.120A pdb=" N TYR M1243 " --> pdb=" O SER M1239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP M1244 " --> pdb=" O LEU M1240 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1239 through 1244' Processing helix chain 'M' and resid 1250 through 1261 Processing helix chain 'M' and resid 1272 through 1286 removed outlier: 3.958A pdb=" N ASP M1276 " --> pdb=" O THR M1272 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL M1277 " --> pdb=" O LYS M1273 " (cutoff:3.500A) Processing helix chain 'M' and resid 1298 through 1310 removed outlier: 4.101A pdb=" N GLN M1302 " --> pdb=" O ILE M1298 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE M1308 " --> pdb=" O LEU M1304 " (cutoff:3.500A) Processing helix chain 'M' and resid 1346 through 1354 removed outlier: 3.762A pdb=" N CYS M1351 " --> pdb=" O MET M1347 " (cutoff:3.500A) Processing helix chain 'M' and resid 1374 through 1386 removed outlier: 3.801A pdb=" N LEU M1380 " --> pdb=" O GLU M1376 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS M1381 " --> pdb=" O SER M1377 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN M1385 " --> pdb=" O LYS M1381 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS M1386 " --> pdb=" O LYS M1382 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 81 removed outlier: 3.988A pdb=" N GLU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 132 through 137 removed outlier: 4.102A pdb=" N PHE R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 132 through 137' Processing helix chain 'R' and resid 138 through 143 removed outlier: 4.086A pdb=" N LYS R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER R 142 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR R 143 " --> pdb=" O THR R 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 138 through 143' Processing helix chain 'R' and resid 219 through 235 Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 308 through 313 removed outlier: 3.969A pdb=" N ILE R 313 " --> pdb=" O GLU R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 317 removed outlier: 3.775A pdb=" N PHE R 317 " --> pdb=" O PRO R 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 314 through 317' Processing helix chain 'R' and resid 329 through 340 removed outlier: 3.531A pdb=" N ALA R 333 " --> pdb=" O GLY R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 350 removed outlier: 3.737A pdb=" N VAL R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 362 removed outlier: 3.772A pdb=" N LEU R 362 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 375 removed outlier: 3.580A pdb=" N ARG R 368 " --> pdb=" O ASN R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 403 Processing helix chain 'R' and resid 407 through 413 removed outlier: 3.974A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 423 through 430 removed outlier: 4.024A pdb=" N CYS R 427 " --> pdb=" O GLY R 423 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 438 removed outlier: 4.278A pdb=" N TRP R 437 " --> pdb=" O GLY R 433 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 61 Processing helix chain 'S' and resid 91 through 107 Processing helix chain 'S' and resid 115 through 125 removed outlier: 3.796A pdb=" N LEU S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 135 removed outlier: 3.631A pdb=" N ILE S 131 " --> pdb=" O PRO S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 192 through 203 removed outlier: 3.517A pdb=" N SER S 203 " --> pdb=" O LYS S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 214 Processing helix chain 'S' and resid 218 through 226 Processing helix chain 'S' and resid 265 through 271 Processing helix chain 'T' and resid 51 through 66 Processing helix chain 'T' and resid 85 through 97 removed outlier: 3.888A pdb=" N GLY T 97 " --> pdb=" O SER T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 111 removed outlier: 4.143A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.580A pdb=" N THR T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 258 Processing helix chain 'T' and resid 264 through 274 removed outlier: 4.162A pdb=" N LYS T 274 " --> pdb=" O GLY T 270 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.732A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 316 Processing helix chain 'T' and resid 317 through 329 removed outlier: 3.578A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 359 Processing helix chain 'T' and resid 360 through 366 removed outlier: 3.535A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 408 Processing helix chain 'T' and resid 411 through 418 removed outlier: 3.873A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.860A pdb=" N CYS T 422 " --> pdb=" O LEU T 418 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY T 423 " --> pdb=" O LEU T 419 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 removed outlier: 4.234A pdb=" N THR T 458 " --> pdb=" O LYS T 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 4.080A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 124 Processing helix chain 'U' and resid 172 through 182 Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 250 through 253 Processing helix chain 'U' and resid 254 through 260 Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.925A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 339 through 343 removed outlier: 3.557A pdb=" N GLY U 342 " --> pdb=" O SER U 339 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU U 343 " --> pdb=" O PRO U 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 339 through 343' Processing helix chain 'U' and resid 344 through 350 removed outlier: 4.059A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 removed outlier: 3.604A pdb=" N ILE U 364 " --> pdb=" O ASN U 360 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS U 365 " --> pdb=" O GLU U 361 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.949A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.585A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'V' and resid 51 through 66 Processing helix chain 'V' and resid 85 through 97 removed outlier: 3.888A pdb=" N GLY V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 111 removed outlier: 4.143A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 129 removed outlier: 3.578A pdb=" N THR V 120 " --> pdb=" O LYS V 116 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 274 removed outlier: 4.163A pdb=" N LYS V 274 " --> pdb=" O GLY V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.732A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 329 removed outlier: 3.579A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 359 Processing helix chain 'V' and resid 360 through 366 removed outlier: 3.535A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 408 Processing helix chain 'V' and resid 411 through 418 removed outlier: 3.872A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 429 removed outlier: 3.860A pdb=" N CYS V 422 " --> pdb=" O LEU V 418 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 removed outlier: 4.234A pdb=" N THR V 458 " --> pdb=" O LYS V 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 93 removed outlier: 4.081A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 124 Processing helix chain 'W' and resid 172 through 182 Processing helix chain 'W' and resid 241 through 248 Processing helix chain 'W' and resid 250 through 253 Processing helix chain 'W' and resid 254 through 260 Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.925A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 339 through 343 removed outlier: 3.557A pdb=" N GLY W 342 " --> pdb=" O SER W 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU W 343 " --> pdb=" O PRO W 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 339 through 343' Processing helix chain 'W' and resid 344 through 350 removed outlier: 4.060A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 removed outlier: 3.604A pdb=" N ILE W 364 " --> pdb=" O ASN W 360 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS W 365 " --> pdb=" O GLU W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.949A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN W 408 " --> pdb=" O SER W 404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG W 413 " --> pdb=" O ILE W 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.586A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'X' and resid 51 through 66 Processing helix chain 'X' and resid 85 through 97 removed outlier: 3.888A pdb=" N GLY X 97 " --> pdb=" O SER X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 111 removed outlier: 4.143A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 129 removed outlier: 3.580A pdb=" N THR X 120 " --> pdb=" O LYS X 116 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE X 129 " --> pdb=" O PHE X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 192 Processing helix chain 'X' and resid 217 through 219 No H-bonds generated for 'chain 'X' and resid 217 through 219' Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 274 removed outlier: 4.163A pdb=" N LYS X 274 " --> pdb=" O GLY X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.733A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 329 removed outlier: 3.578A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU X 329 " --> pdb=" O ASN X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 359 Processing helix chain 'X' and resid 360 through 366 removed outlier: 3.535A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 408 Processing helix chain 'X' and resid 411 through 418 removed outlier: 3.873A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 429 removed outlier: 3.861A pdb=" N CYS X 422 " --> pdb=" O LEU X 418 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY X 423 " --> pdb=" O LEU X 419 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 removed outlier: 4.233A pdb=" N THR X 458 " --> pdb=" O LYS X 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 4.081A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 124 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 248 Processing helix chain 'Y' and resid 250 through 253 Processing helix chain 'Y' and resid 254 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.925A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 339 through 343 removed outlier: 3.557A pdb=" N GLY Y 342 " --> pdb=" O SER Y 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Y 343 " --> pdb=" O PRO Y 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 339 through 343' Processing helix chain 'Y' and resid 344 through 350 removed outlier: 4.059A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 removed outlier: 3.603A pdb=" N ILE Y 364 " --> pdb=" O ASN Y 360 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Y 365 " --> pdb=" O GLU Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.949A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.586A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 Processing sheet with id=AA1, first strand: chain 'Z' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.383A pdb=" N ARG A 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 84 removed outlier: 7.323A pdb=" N ARG B 83 " --> pdb=" O VAL C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'E' and resid 43 through 44 removed outlier: 7.287A pdb=" N ARG E 43 " --> pdb=" O ILE G 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 78 through 79 Processing sheet with id=AA8, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.982A pdb=" N ARG F 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'M' and resid 718 through 719 removed outlier: 6.482A pdb=" N MET M 821 " --> pdb=" O LEU M 849 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU M 851 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU M 823 " --> pdb=" O LEU M 851 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU M 749 " --> pdb=" O VAL M 822 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ASP M 824 " --> pdb=" O LEU M 749 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL M 751 " --> pdb=" O ASP M 824 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL M 801 " --> pdb=" O ILE M 750 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 944 through 946 removed outlier: 6.224A pdb=" N TYR M 945 " --> pdb=" O ILE M1366 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA M1265 " --> pdb=" O PHE M1317 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU M1319 " --> pdb=" O ALA M1265 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE M1267 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET M1290 " --> pdb=" O ILE M1318 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N SER M1320 " --> pdb=" O MET M1290 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 949 through 951 removed outlier: 6.036A pdb=" N VAL M 949 " --> pdb=" O VAL M1370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'R' and resid 26 through 29 removed outlier: 3.614A pdb=" N PHE R 17 " --> pdb=" O PHE R 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA R 28 " --> pdb=" O ILE R 15 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE R 6 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU R 99 " --> pdb=" O PHE R 129 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 128 " --> pdb=" O VAL R 414 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL R 414 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 40 through 41 removed outlier: 4.009A pdb=" N ALA R 33 " --> pdb=" O TYR R 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 147 through 151 removed outlier: 5.965A pdb=" N ILE R 353 " --> pdb=" O SER R 386 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS R 355 " --> pdb=" O PRO R 388 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 147 through 151 removed outlier: 5.965A pdb=" N ILE R 353 " --> pdb=" O SER R 386 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS R 355 " --> pdb=" O PRO R 388 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 286 through 288 removed outlier: 4.084A pdb=" N TYR R 286 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL R 275 " --> pdb=" O TYR R 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 5 through 7 removed outlier: 6.628A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 5 through 7 removed outlier: 6.628A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU V 135 " --> pdb=" O ILE V 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS V 137 " --> pdb=" O LYS V 241 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 102 through 106 removed outlier: 4.046A pdb=" N LEU T 308 " --> pdb=" O VAL T 335 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA T 78 " --> pdb=" O VAL T 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 246 through 248 removed outlier: 3.645A pdb=" N VAL T 247 " --> pdb=" O LEU T 131 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU T 131 " --> pdb=" O VAL T 247 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG T 132 " --> pdb=" O GLU T 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU T 302 " --> pdb=" O ARG T 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 176 through 180 removed outlier: 6.628A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY T 142 " --> pdb=" O ILE T 200 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 176 through 180 removed outlier: 6.628A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU T 135 " --> pdb=" O ILE T 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS T 137 " --> pdb=" O LYS T 241 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS T 241 " --> pdb=" O LYS T 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 345 through 346 Processing sheet with id=AC7, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.690A pdb=" N SER U 41 " --> pdb=" O MET U 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 98 through 102 removed outlier: 5.951A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 166 through 171 removed outlier: 3.713A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU U 142 " --> pdb=" O THR U 159 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 199 through 204 removed outlier: 6.331A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL U 140 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE U 190 " --> pdb=" O GLY U 138 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY U 138 " --> pdb=" O ILE U 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 102 through 106 removed outlier: 4.046A pdb=" N LEU V 308 " --> pdb=" O VAL V 335 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA V 78 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 246 through 248 removed outlier: 3.644A pdb=" N VAL V 247 " --> pdb=" O LEU V 131 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU V 131 " --> pdb=" O VAL V 247 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG V 132 " --> pdb=" O GLU V 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU V 302 " --> pdb=" O ARG V 132 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 345 through 346 Processing sheet with id=AD5, first strand: chain 'W' and resid 40 through 41 removed outlier: 3.690A pdb=" N SER W 41 " --> pdb=" O MET W 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 98 through 102 removed outlier: 5.951A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 166 through 171 removed outlier: 3.712A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 199 through 204 removed outlier: 6.332A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL W 140 " --> pdb=" O ASP W 188 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY W 138 " --> pdb=" O ILE W 190 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 102 through 106 removed outlier: 4.047A pdb=" N LEU X 308 " --> pdb=" O VAL X 335 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA X 78 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 246 through 248 removed outlier: 3.644A pdb=" N VAL X 247 " --> pdb=" O LEU X 131 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU X 131 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG X 132 " --> pdb=" O GLU X 302 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 302 " --> pdb=" O ARG X 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 176 through 180 removed outlier: 6.628A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP X 198 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU X 203 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL X 209 " --> pdb=" O GLU X 203 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 176 through 180 removed outlier: 6.628A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU X 135 " --> pdb=" O ILE X 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS X 137 " --> pdb=" O LYS X 241 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 345 through 346 Processing sheet with id=AE5, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.690A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 98 through 102 removed outlier: 5.951A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 166 through 171 removed outlier: 3.712A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 199 through 204 removed outlier: 6.331A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY Y 203 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL Y 140 " --> pdb=" O ASP Y 188 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE Y 190 " --> pdb=" O GLY Y 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY Y 138 " --> pdb=" O ILE Y 190 " (cutoff:3.500A) 1650 hydrogen bonds defined for protein. 4839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 421 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 15.80 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11615 1.34 - 1.46: 9372 1.46 - 1.58: 23975 1.58 - 1.70: 716 1.70 - 1.82: 194 Bond restraints: 45872 Sorted by residual: bond pdb=" C VAL S 116 " pdb=" N PRO S 117 " ideal model delta sigma weight residual 1.337 1.401 -0.065 1.11e-02 8.12e+03 3.39e+01 bond pdb=" F2 BEF R 502 " pdb="BE BEF R 502 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" F2 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5' DA I -54 " pdb=" C4' DA I -54 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.52e+01 bond pdb=" C1' DT J -46 " pdb=" N1 DT J -46 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.48e+01 ... (remaining 45867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 62821 2.84 - 5.68: 643 5.68 - 8.51: 80 8.51 - 11.35: 8 11.35 - 14.19: 4 Bond angle restraints: 63556 Sorted by residual: angle pdb=" C PHE R 136 " pdb=" N VAL R 137 " pdb=" CA VAL R 137 " ideal model delta sigma weight residual 120.24 124.26 -4.02 6.30e-01 2.52e+00 4.07e+01 angle pdb=" O4' DG I 48 " pdb=" C4' DG I 48 " pdb=" C3' DG I 48 " ideal model delta sigma weight residual 106.00 102.35 3.65 6.00e-01 2.78e+00 3.71e+01 angle pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta sigma weight residual 126.32 135.68 -9.36 1.74e+00 3.30e-01 2.89e+01 angle pdb=" N LYS X 161 " pdb=" CA LYS X 161 " pdb=" C LYS X 161 " ideal model delta sigma weight residual 107.23 115.43 -8.20 1.67e+00 3.59e-01 2.41e+01 angle pdb=" C VAL M1068 " pdb=" N LYS M1069 " pdb=" CA LYS M1069 " ideal model delta sigma weight residual 123.93 131.43 -7.50 1.54e+00 4.22e-01 2.37e+01 ... (remaining 63551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 24847 35.71 - 71.42: 2108 71.42 - 107.12: 51 107.12 - 142.83: 11 142.83 - 178.54: 4 Dihedral angle restraints: 27021 sinusoidal: 13070 harmonic: 13951 Sorted by residual: dihedral pdb=" CA GLY T 160 " pdb=" C GLY T 160 " pdb=" N LYS T 161 " pdb=" CA LYS T 161 " ideal model delta harmonic sigma weight residual -180.00 -126.60 -53.40 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASP X 151 " pdb=" C ASP X 151 " pdb=" N ALA X 152 " pdb=" CA ALA X 152 " ideal model delta harmonic sigma weight residual -180.00 -131.00 -49.00 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA PHE W 221 " pdb=" C PHE W 221 " pdb=" N VAL W 222 " pdb=" CA VAL W 222 " ideal model delta harmonic sigma weight residual 180.00 131.98 48.02 0 5.00e+00 4.00e-02 9.22e+01 ... (remaining 27018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5500 0.045 - 0.090: 1441 0.090 - 0.135: 453 0.135 - 0.180: 34 0.180 - 0.225: 12 Chirality restraints: 7440 Sorted by residual: chirality pdb=" CA PHE M 999 " pdb=" N PHE M 999 " pdb=" C PHE M 999 " pdb=" CB PHE M 999 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" P DT J 25 " pdb=" OP1 DT J 25 " pdb=" OP2 DT J 25 " pdb=" O5' DT J 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ARG M1133 " pdb=" N ARG M1133 " pdb=" C ARG M1133 " pdb=" CB ARG M1133 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 7437 not shown) Planarity restraints: 6874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER W 205 " 0.040 2.00e-02 2.50e+03 8.23e-02 6.77e+01 pdb=" C SER W 205 " -0.142 2.00e-02 2.50e+03 pdb=" O SER W 205 " 0.055 2.00e-02 2.50e+03 pdb=" N PHE W 206 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Y 205 " 0.035 2.00e-02 2.50e+03 6.97e-02 4.86e+01 pdb=" C SER Y 205 " -0.121 2.00e-02 2.50e+03 pdb=" O SER Y 205 " 0.046 2.00e-02 2.50e+03 pdb=" N PHE Y 206 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP X 151 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C ASP X 151 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP X 151 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA X 152 " -0.024 2.00e-02 2.50e+03 ... (remaining 6871 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 959 2.67 - 3.23: 36799 3.23 - 3.78: 71964 3.78 - 4.34: 94279 4.34 - 4.90: 146083 Nonbonded interactions: 350084 Sorted by model distance: nonbonded pdb=" O3B ADP M1601 " pdb="BE BEF M1602 " model vdw 2.109 1.936 nonbonded pdb=" O1B ADP R 501 " pdb="MG MG R 503 " model vdw 2.170 2.170 nonbonded pdb=" O3B ADP X 501 " pdb="MG MG Y 501 " model vdw 2.178 2.170 nonbonded pdb=" F3 BEF M1602 " pdb="MG MG M1603 " model vdw 2.192 2.120 nonbonded pdb=" O3B ADP T 501 " pdb="MG MG U 501 " model vdw 2.237 2.170 ... (remaining 350079 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' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 17 through 117) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 501)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 501)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 501)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459 or resid 502 throug \ h 503)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 502)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9 or resid 502 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.060 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.140 Process input model: 58.980 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 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 : 0.009 0.901 45882 Z= 0.707 Angle : 0.848 37.602 63565 Z= 0.573 Chirality : 0.045 0.225 7440 Planarity : 0.005 0.082 6874 Dihedral : 20.637 178.540 17991 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 8.77 % Allowed : 8.39 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.38 % 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 are not related in a simple way. whole: -4.51 (0.09), residues: 4633 helix: -3.92 (0.05), residues: 2130 sheet: -0.77 (0.20), residues: 580 loop : -2.36 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 208 TYR 0.029 0.001 TYR V 462 PHE 0.014 0.001 PHE M1047 TRP 0.010 0.001 TRP M 790 HIS 0.007 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.35 (45872) covalent geometry : angle 0.81255 / 0.57 (63556) hydrogen bonds : bond 0.14567 / 9.21 ( 2038) hydrogen bonds : angle 9.25728 / 6.25 ( 5641) metal coordination : bond 0.37033 / 18.61 ( 8) metal coordination : angle 20.51469 / 9.95 ( 9) Misc. bond : bond 0.89996 / 45.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1505 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 350 poor density : 1155 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.4546 (mt) cc_final: 0.4320 (mt) REVERT: B 131 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7979 (mtp85) REVERT: C 70 VAL cc_start: 0.8574 (t) cc_final: 0.8325 (t) REVERT: D 67 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.8151 (ttp-110) REVERT: E 57 GLU cc_start: 0.7603 (tt0) cc_final: 0.6653 (tt0) REVERT: F 93 GLU cc_start: 0.8648 (mp0) cc_final: 0.8429 (mp0) REVERT: F 94 LEU cc_start: 0.8695 (mt) cc_final: 0.8450 (mt) REVERT: H 72 ILE cc_start: 0.8832 (mm) cc_final: 0.8346 (mm) REVERT: M 794 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (p0) REVERT: M 937 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6813 (t) REVERT: M 1039 ASP cc_start: 0.7924 (t70) cc_final: 0.7482 (t0) REVERT: M 1054 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7332 (tp) REVERT: M 1082 ASN cc_start: 0.6472 (OUTLIER) cc_final: 0.6088 (m-40) REVERT: M 1192 MET cc_start: 0.6490 (tpt) cc_final: 0.6278 (tpt) REVERT: M 1326 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7638 (tp) REVERT: R 226 LEU cc_start: 0.8111 (tp) cc_final: 0.7688 (tp) REVERT: R 230 THR cc_start: 0.7902 (p) cc_final: 0.7673 (t) REVERT: R 408 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: S 12 THR cc_start: 0.8160 (m) cc_final: 0.7784 (m) REVERT: S 49 ILE cc_start: 0.7094 (mt) cc_final: 0.6619 (mm) REVERT: S 175 ILE cc_start: 0.8726 (mt) cc_final: 0.8508 (pt) REVERT: S 278 ARG cc_start: 0.5531 (mmt-90) cc_final: 0.5088 (tpm170) REVERT: T 133 ILE cc_start: -0.3733 (OUTLIER) cc_final: -0.4011 (mt) REVERT: T 182 ASP cc_start: 0.3031 (OUTLIER) cc_final: 0.2650 (t70) REVERT: T 202 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4850 (tt) REVERT: T 226 THR cc_start: 0.5115 (OUTLIER) cc_final: 0.4731 (t) REVERT: T 233 PRO cc_start: 0.0224 (Cg_exo) cc_final: -0.0107 (Cg_endo) REVERT: T 456 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6732 (tp) REVERT: U 15 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.4992 (tptp) REVERT: U 136 ILE cc_start: 0.7432 (mt) cc_final: 0.7107 (tp) REVERT: U 252 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.3094 (tt0) REVERT: U 259 THR cc_start: 0.6839 (p) cc_final: 0.6277 (p) REVERT: V 24 THR cc_start: 0.7758 (m) cc_final: 0.7356 (p) REVERT: V 247 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (p) REVERT: V 317 ASP cc_start: 0.8497 (t0) cc_final: 0.8261 (t70) REVERT: W 160 ILE cc_start: 0.8608 (mt) cc_final: 0.8273 (tp) REVERT: W 255 LEU cc_start: 0.8307 (mt) cc_final: 0.7946 (tp) REVERT: W 420 VAL cc_start: 0.6609 (OUTLIER) cc_final: 0.6051 (t) REVERT: X 153 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: X 162 THR cc_start: -0.0253 (OUTLIER) cc_final: -0.1004 (p) REVERT: X 163 ILE cc_start: 0.0102 (OUTLIER) cc_final: -0.0589 (mt) REVERT: Y 117 LEU cc_start: 0.7518 (tp) cc_final: 0.7226 (tp) REVERT: Y 135 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6981 (tt) REVERT: Y 160 ILE cc_start: 0.8727 (mt) cc_final: 0.8509 (tp) REVERT: Y 268 GLU cc_start: 0.2283 (OUTLIER) cc_final: -0.0626 (mm-30) REVERT: Y 456 ILE cc_start: 0.0232 (OUTLIER) cc_final: -0.0087 (pt) outliers start: 350 outliers final: 41 residues processed: 1423 average time/residue: 0.2996 time to fit residues: 681.0618 Evaluate side-chains 560 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 499 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain M residue 794 ASP Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1038 VAL Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1054 LEU Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1213 VAL Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 322 THR Chi-restraints excluded: chain T residue 456 LEU Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 292 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 206 PHE Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 153 GLU Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 221 PHE Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 494 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 113 HIS E 16 GLN E 39 ASN E 42 GLN E 113 HIS F 32 HIS F 39 ASN G 112 HIS H 112 HIS M 730 GLN M 782 GLN M 857 GLN M1070 ASN M1226 GLN M1249 GLN M1352 GLN R 45 HIS R 61 HIS ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 HIS ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN R 247 ASN R 251 GLN R 359 ASN S 279 ASN T 124 ASN ** T 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 263 GLN T 271 GLN T 289 ASN ** T 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 ASN U 237 HIS U 252 GLN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN U 455 GLN V 190 GLN V 245 GLN V 271 GLN ** V 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 341 ASN V 357 HIS ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 272 GLN W 299 HIS W 401 ASN W 416 ASN W 455 GLN X 271 GLN X 289 ASN X 341 ASN X 357 HIS Y 23 HIS ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 230 GLN Y 326 ASN Y 408 GLN Y 455 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.094541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.078604 restraints weight = 311655.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.080414 restraints weight = 194137.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.081613 restraints weight = 134715.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.082369 restraints weight = 101903.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.082965 restraints weight = 82977.183| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 45882 Z= 0.262 Angle : 0.891 15.767 63565 Z= 0.461 Chirality : 0.050 0.267 7440 Planarity : 0.007 0.098 6874 Dihedral : 24.301 162.270 9136 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 5.81 % Allowed : 18.16 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 are not related in a simple way. whole: -2.41 (0.11), residues: 4633 helix: -1.50 (0.09), residues: 2148 sheet: -0.41 (0.20), residues: 619 loop : -1.99 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG Y 204 TYR 0.029 0.003 TYR Y 447 PHE 0.030 0.003 PHE H 68 TRP 0.021 0.002 TRP M 790 HIS 0.024 0.003 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.26 (45872) covalent geometry : angle 0.88600 / 0.46 (63556) hydrogen bonds : bond 0.06675 / 4.01 ( 2038) hydrogen bonds : angle 5.47861 / 3.72 ( 5641) metal coordination : bond 0.02348 / 1.36 ( 8) metal coordination : angle 7.85756 / 4.17 ( 9) Misc. bond : bond 0.01994 / 1.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 487 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8407 (pt0) cc_final: 0.8179 (pt0) REVERT: E 57 GLU cc_start: 0.7873 (tt0) cc_final: 0.7499 (tt0) REVERT: F 93 GLU cc_start: 0.9271 (mp0) cc_final: 0.8943 (mp0) REVERT: G 38 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: G 46 LYS cc_start: 0.9352 (mmmt) cc_final: 0.8851 (tptt) REVERT: G 108 GLU cc_start: 0.8356 (mp0) cc_final: 0.7983 (tp30) REVERT: H 102 ARG cc_start: 0.8360 (mmm160) cc_final: 0.8109 (mmm160) REVERT: H 111 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7783 (mtmt) REVERT: M 821 MET cc_start: 0.4684 (ptt) cc_final: 0.4311 (ptp) REVERT: M 937 VAL cc_start: 0.6581 (OUTLIER) cc_final: 0.5705 (t) REVERT: M 999 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.4031 (m-80) REVERT: M 1054 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7144 (tp) REVERT: M 1082 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.6337 (t0) REVERT: R 192 ASP cc_start: 0.8631 (p0) cc_final: 0.8282 (t0) REVERT: R 238 MET cc_start: 0.7301 (tpp) cc_final: 0.6841 (tpt) REVERT: S 12 THR cc_start: 0.8652 (m) cc_final: 0.7980 (m) REVERT: S 278 ARG cc_start: 0.6345 (mmt-90) cc_final: 0.5289 (tpm170) REVERT: T 70 MET cc_start: 0.1898 (mmt) cc_final: 0.0796 (ttm) REVERT: T 182 ASP cc_start: 0.3484 (OUTLIER) cc_final: 0.2476 (t70) REVERT: U 15 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.6050 (tptp) REVERT: V 24 THR cc_start: 0.8187 (m) cc_final: 0.7923 (p) REVERT: V 31 LYS cc_start: 0.8926 (mttt) cc_final: 0.8644 (mtmt) REVERT: V 111 TYR cc_start: 0.6756 (m-80) cc_final: 0.5284 (m-80) REVERT: V 221 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7718 (pp20) REVERT: V 245 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8357 (pp30) REVERT: V 367 LEU cc_start: 0.8629 (mt) cc_final: 0.8293 (mt) REVERT: W 245 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8683 (t0) REVERT: W 255 LEU cc_start: 0.8551 (mt) cc_final: 0.8110 (tp) REVERT: X 70 MET cc_start: 0.4434 (ppp) cc_final: 0.3830 (mmt) REVERT: X 73 ARG cc_start: 0.7326 (mmt-90) cc_final: 0.6839 (ptt180) REVERT: X 150 GLU cc_start: 0.2152 (OUTLIER) cc_final: 0.1739 (pt0) REVERT: X 315 MET cc_start: 0.1196 (tmm) cc_final: 0.0336 (ppp) REVERT: X 329 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8087 (mm-30) REVERT: X 335 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.6826 (t) REVERT: X 431 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6848 (mtp180) REVERT: Y 160 ILE cc_start: 0.8791 (mt) cc_final: 0.8432 (tp) REVERT: Y 213 ASP cc_start: 0.2979 (OUTLIER) cc_final: 0.1770 (t0) REVERT: Y 456 ILE cc_start: -0.2047 (OUTLIER) cc_final: -0.2529 (pt) outliers start: 232 outliers final: 109 residues processed: 679 average time/residue: 0.2647 time to fit residues: 301.3475 Evaluate side-chains 484 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 361 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 735 LEU Chi-restraints excluded: chain M residue 757 LEU Chi-restraints excluded: chain M residue 823 LEU Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1048 THR Chi-restraints excluded: chain M residue 1054 LEU Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1204 SER Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain R residue 428 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 372 THR Chi-restraints excluded: chain T residue 461 ASN Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain W residue 19 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 335 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 273 ILE Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 364 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 502 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 426 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN M1044 ASN M1070 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 289 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 279 ASN T 205 ASN T 325 ASN T 461 ASN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 GLN V 341 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Y 299 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.099318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.083448 restraints weight = 345638.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.085171 restraints weight = 213284.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.086296 restraints weight = 147636.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.087057 restraints weight = 111438.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.087590 restraints weight = 90468.864| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 45882 Z= 0.164 Angle : 0.712 13.712 63565 Z= 0.369 Chirality : 0.045 0.245 7440 Planarity : 0.005 0.112 6874 Dihedral : 24.139 162.405 9093 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.31 % Allowed : 18.44 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 are not related in a simple way. whole: -1.60 (0.11), residues: 4633 helix: -0.57 (0.10), residues: 2159 sheet: -0.32 (0.20), residues: 622 loop : -1.82 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 122 TYR 0.035 0.002 TYR U 439 PHE 0.031 0.002 PHE X 321 TRP 0.012 0.001 TRP M 790 HIS 0.018 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (45872) covalent geometry : angle 0.70875 / 0.37 (63556) hydrogen bonds : bond 0.05499 / 3.28 ( 2038) hydrogen bonds : angle 4.90208 / 3.33 ( 5641) metal coordination : bond 0.00528 / 0.30 ( 8) metal coordination : angle 6.07271 / 3.22 ( 9) Misc. bond : bond 0.00592 / 0.31 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 403 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLN cc_start: 0.9343 (tp40) cc_final: 0.8596 (tm-30) REVERT: B 83 ARG cc_start: 0.7831 (mmt90) cc_final: 0.7260 (mtt-85) REVERT: C 59 LYS cc_start: 0.9388 (tptm) cc_final: 0.8795 (tptp) REVERT: E 57 GLU cc_start: 0.7924 (tt0) cc_final: 0.7568 (tt0) REVERT: F 93 GLU cc_start: 0.9264 (mp0) cc_final: 0.8862 (mp0) REVERT: G 46 LYS cc_start: 0.9362 (mmmt) cc_final: 0.8872 (tptt) REVERT: G 79 GLU cc_start: 0.8193 (tp30) cc_final: 0.7882 (tt0) REVERT: G 108 GLU cc_start: 0.8363 (mp0) cc_final: 0.8009 (tp30) REVERT: H 70 ASN cc_start: 0.8550 (m110) cc_final: 0.8221 (m-40) REVERT: H 102 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8100 (mmm160) REVERT: H 111 LYS cc_start: 0.8094 (ttpm) cc_final: 0.7884 (mtmt) REVERT: M 764 PHE cc_start: 0.7972 (m-80) cc_final: 0.7738 (m-80) REVERT: M 821 MET cc_start: 0.4486 (ptt) cc_final: 0.4235 (ptp) REVERT: M 1326 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7439 (tp) REVERT: R 192 ASP cc_start: 0.8391 (p0) cc_final: 0.8122 (t0) REVERT: R 226 LEU cc_start: 0.8536 (tp) cc_final: 0.8191 (tp) REVERT: R 238 MET cc_start: 0.7094 (tpp) cc_final: 0.6793 (tpt) REVERT: S 20 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8209 (t) REVERT: S 278 ARG cc_start: 0.6158 (mmt-90) cc_final: 0.4909 (tpm170) REVERT: T 70 MET cc_start: 0.2360 (OUTLIER) cc_final: 0.1464 (ttm) REVERT: T 182 ASP cc_start: 0.3133 (OUTLIER) cc_final: 0.2137 (t70) REVERT: T 385 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8211 (mt-10) REVERT: U 15 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6152 (tptp) REVERT: U 118 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9045 (p) REVERT: U 185 LEU cc_start: 0.7752 (mt) cc_final: 0.7515 (tp) REVERT: V 24 THR cc_start: 0.8000 (m) cc_final: 0.7778 (p) REVERT: V 221 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7673 (tp30) REVERT: V 266 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7949 (tp) REVERT: V 367 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8152 (mt) REVERT: V 406 MET cc_start: 0.8844 (tpp) cc_final: 0.8512 (mmm) REVERT: W 154 LYS cc_start: 0.6571 (mttp) cc_final: 0.6123 (mmtm) REVERT: W 206 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.6021 (p90) REVERT: W 255 LEU cc_start: 0.8213 (mt) cc_final: 0.7811 (tp) REVERT: X 315 MET cc_start: 0.1712 (OUTLIER) cc_final: 0.1149 (ppp) REVERT: X 329 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7912 (mm-30) REVERT: X 431 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6966 (mtp180) REVERT: Y 160 ILE cc_start: 0.8846 (mt) cc_final: 0.8538 (tp) REVERT: Y 198 LYS cc_start: 0.4552 (OUTLIER) cc_final: 0.4061 (mtmm) REVERT: Y 213 ASP cc_start: 0.2737 (OUTLIER) cc_final: 0.1371 (t0) REVERT: Y 268 GLU cc_start: 0.2382 (OUTLIER) cc_final: -0.0091 (mm-30) REVERT: Y 456 ILE cc_start: -0.1694 (OUTLIER) cc_final: -0.2302 (pt) outliers start: 212 outliers final: 121 residues processed: 572 average time/residue: 0.2583 time to fit residues: 249.5851 Evaluate side-chains 477 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 342 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 871 MET Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1233 ILE Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1343 TRP Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 279 ASN Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 266 ILE Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 206 PHE Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 315 MET Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 273 ILE Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 90 optimal weight: 30.0000 chunk 240 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 409 optimal weight: 7.9990 chunk 428 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 27 GLN D 75 HIS H 70 ASN M1070 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 461 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 256 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN X 341 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.097783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.081896 restraints weight = 347387.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.083621 restraints weight = 212529.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.084752 restraints weight = 145990.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.085484 restraints weight = 109932.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.085933 restraints weight = 89338.594| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45882 Z= 0.158 Angle : 0.692 10.266 63565 Z= 0.358 Chirality : 0.044 0.285 7440 Planarity : 0.004 0.050 6874 Dihedral : 23.970 168.071 9087 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.09 % Allowed : 19.01 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.19 (0.11), residues: 4633 helix: -0.07 (0.11), residues: 2153 sheet: -0.33 (0.21), residues: 607 loop : -1.73 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 92 TYR 0.033 0.002 TYR C 88 PHE 0.031 0.002 PHE X 321 TRP 0.013 0.001 TRP M1343 HIS 0.015 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (45872) covalent geometry : angle 0.69014 / 0.36 (63556) hydrogen bonds : bond 0.05324 / 3.16 ( 2038) hydrogen bonds : angle 4.62535 / 3.13 ( 5641) metal coordination : bond 0.00582 / 0.33 ( 8) metal coordination : angle 4.46854 / 2.31 ( 9) Misc. bond : bond 0.00695 / 0.36 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 372 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLN cc_start: 0.9278 (tp40) cc_final: 0.8647 (tm-30) REVERT: B 83 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7228 (mtt180) REVERT: C 67 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6939 (tpm170) REVERT: D 55 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6303 (mtt-85) REVERT: E 57 GLU cc_start: 0.7983 (tt0) cc_final: 0.7644 (tt0) REVERT: G 46 LYS cc_start: 0.9337 (mmmt) cc_final: 0.8864 (tptt) REVERT: G 79 GLU cc_start: 0.8166 (tp30) cc_final: 0.7745 (tt0) REVERT: H 70 ASN cc_start: 0.8654 (m-40) cc_final: 0.8250 (m-40) REVERT: H 96 GLU cc_start: 0.8624 (mp0) cc_final: 0.7493 (mp0) REVERT: H 102 ARG cc_start: 0.8315 (mmm160) cc_final: 0.8101 (mmm160) REVERT: H 111 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7780 (mtmt) REVERT: M 764 PHE cc_start: 0.8008 (m-80) cc_final: 0.7654 (m-80) REVERT: M 821 MET cc_start: 0.4660 (ptt) cc_final: 0.4400 (ptp) REVERT: R 226 LEU cc_start: 0.8549 (tp) cc_final: 0.8238 (tp) REVERT: R 238 MET cc_start: 0.7354 (tpp) cc_final: 0.6896 (tpt) REVERT: S 278 ARG cc_start: 0.6380 (mmt-90) cc_final: 0.5039 (tpm170) REVERT: T 70 MET cc_start: 0.2387 (mmt) cc_final: 0.1602 (ttm) REVERT: T 76 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5100 (pt) REVERT: T 182 ASP cc_start: 0.3759 (OUTLIER) cc_final: 0.3233 (t70) REVERT: T 194 VAL cc_start: -0.2821 (OUTLIER) cc_final: -0.3091 (t) REVERT: T 385 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8161 (mt-10) REVERT: U 44 MET cc_start: 0.5992 (mmm) cc_final: 0.5752 (mmt) REVERT: U 323 MET cc_start: 0.7743 (mtm) cc_final: 0.7268 (mtm) REVERT: V 24 THR cc_start: 0.7954 (m) cc_final: 0.7720 (p) REVERT: V 266 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8072 (tp) REVERT: V 406 MET cc_start: 0.8736 (tpp) cc_final: 0.8469 (mmm) REVERT: W 255 LEU cc_start: 0.8252 (mt) cc_final: 0.7842 (tp) REVERT: X 284 LEU cc_start: 0.7419 (tp) cc_final: 0.7194 (tp) REVERT: X 315 MET cc_start: 0.2268 (OUTLIER) cc_final: 0.1689 (ppp) REVERT: X 329 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7827 (mp0) REVERT: X 431 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7275 (mtp180) REVERT: Y 117 LEU cc_start: 0.8461 (tp) cc_final: 0.8217 (tp) REVERT: Y 160 ILE cc_start: 0.8925 (mt) cc_final: 0.8621 (tp) REVERT: Y 198 LYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4232 (mtmm) REVERT: Y 268 GLU cc_start: 0.2683 (OUTLIER) cc_final: 0.0102 (mm-30) outliers start: 203 outliers final: 143 residues processed: 534 average time/residue: 0.2372 time to fit residues: 215.2961 Evaluate side-chains 488 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 336 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 871 MET Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1304 LEU Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 461 ASN Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 137 GLU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 317 PHE Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 251 ASP Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 266 ILE Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain W residue 454 VAL Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 315 MET Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 367 LEU Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 273 ILE Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 130 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 281 optimal weight: 0.0670 chunk 365 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 337 optimal weight: 9.9990 chunk 394 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 GLN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 325 ASN U 119 GLN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 373 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.096386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.081618 restraints weight = 345810.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.082566 restraints weight = 235832.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.083851 restraints weight = 166846.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.084310 restraints weight = 105203.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.084403 restraints weight = 97576.807| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 45882 Z= 0.161 Angle : 0.689 11.893 63565 Z= 0.357 Chirality : 0.044 0.293 7440 Planarity : 0.004 0.053 6874 Dihedral : 23.892 171.595 9083 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.16 % Allowed : 19.26 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -0.95 (0.12), residues: 4633 helix: 0.21 (0.11), residues: 2163 sheet: -0.38 (0.21), residues: 617 loop : -1.68 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 126 TYR 0.044 0.002 TYR G 86 PHE 0.024 0.001 PHE H 68 TRP 0.012 0.001 TRP M1343 HIS 0.017 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (45872) covalent geometry : angle 0.68768 / 0.36 (63556) hydrogen bonds : bond 0.05261 / 3.10 ( 2038) hydrogen bonds : angle 4.51851 / 3.05 ( 5641) metal coordination : bond 0.00723 / 0.36 ( 8) metal coordination : angle 3.69236 / 1.93 ( 9) Misc. bond : bond 0.00290 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 358 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8389 (pt0) cc_final: 0.8182 (tp30) REVERT: B 68 GLN cc_start: 0.9217 (tp40) cc_final: 0.8615 (tm-30) REVERT: B 83 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7446 (mmt180) REVERT: C 67 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6740 (tpm170) REVERT: D 55 ARG cc_start: 0.6659 (mtt180) cc_final: 0.6261 (mtt-85) REVERT: E 57 GLU cc_start: 0.7946 (tt0) cc_final: 0.7604 (tt0) REVERT: G 46 LYS cc_start: 0.9343 (mmmt) cc_final: 0.8858 (tptt) REVERT: H 70 ASN cc_start: 0.8749 (m-40) cc_final: 0.8322 (m110) REVERT: H 111 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: M 764 PHE cc_start: 0.8052 (m-80) cc_final: 0.7706 (m-80) REVERT: M 821 MET cc_start: 0.4858 (ptt) cc_final: 0.4657 (ptp) REVERT: M 1005 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7821 (tt) REVERT: M 1131 ASP cc_start: 0.8695 (t0) cc_final: 0.8242 (t70) REVERT: M 1197 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8868 (mm) REVERT: M 1326 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7534 (tp) REVERT: R 226 LEU cc_start: 0.8590 (tp) cc_final: 0.8252 (tp) REVERT: R 238 MET cc_start: 0.7303 (tpp) cc_final: 0.6974 (tpt) REVERT: S 278 ARG cc_start: 0.6314 (mmt-90) cc_final: 0.5103 (tpm170) REVERT: T 70 MET cc_start: 0.2861 (OUTLIER) cc_final: 0.2226 (ttm) REVERT: T 76 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.4986 (pt) REVERT: T 105 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6433 (tp) REVERT: V 221 GLU cc_start: 0.8164 (tp30) cc_final: 0.7920 (mm-30) REVERT: V 406 MET cc_start: 0.8784 (tpp) cc_final: 0.8522 (mmm) REVERT: W 255 LEU cc_start: 0.8250 (mt) cc_final: 0.7830 (tp) REVERT: X 116 LYS cc_start: 0.4381 (pttt) cc_final: 0.3400 (tptt) REVERT: X 146 GLU cc_start: -0.4044 (OUTLIER) cc_final: -0.4391 (pt0) REVERT: X 315 MET cc_start: 0.2024 (OUTLIER) cc_final: 0.1579 (ppp) REVERT: X 406 MET cc_start: 0.8372 (mmm) cc_final: 0.8087 (mmm) REVERT: X 431 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7568 (mtp180) REVERT: Y 117 LEU cc_start: 0.8479 (tp) cc_final: 0.8273 (tp) REVERT: Y 198 LYS cc_start: 0.4692 (OUTLIER) cc_final: 0.4234 (mtmm) REVERT: Y 268 GLU cc_start: 0.2830 (OUTLIER) cc_final: 0.0314 (mm-30) outliers start: 206 outliers final: 139 residues processed: 522 average time/residue: 0.2207 time to fit residues: 195.4919 Evaluate side-chains 476 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 325 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 871 MET Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1347 MET Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 137 GLU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 251 ASP Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 108 SER Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 315 MET Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 101 ILE Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 259 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 440 optimal weight: 6.9990 chunk 368 optimal weight: 0.0870 chunk 87 optimal weight: 40.0000 chunk 195 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 483 optimal weight: 0.6980 chunk 312 optimal weight: 10.0000 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 25 ASN F 42 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 106 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN V 29 HIS ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 205 ASN ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.093573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.077641 restraints weight = 348388.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.079295 restraints weight = 212839.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.080384 restraints weight = 146649.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.081139 restraints weight = 110843.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.081528 restraints weight = 90133.368| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45882 Z= 0.187 Angle : 0.728 16.395 63565 Z= 0.376 Chirality : 0.045 0.281 7440 Planarity : 0.005 0.070 6874 Dihedral : 23.822 177.859 9076 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.06 % Allowed : 19.84 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.86 (0.12), residues: 4633 helix: 0.35 (0.11), residues: 2173 sheet: -0.42 (0.20), residues: 639 loop : -1.72 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 126 TYR 0.054 0.002 TYR C 88 PHE 0.025 0.002 PHE H 68 TRP 0.015 0.002 TRP U 280 HIS 0.010 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (45872) covalent geometry : angle 0.72690 / 0.38 (63556) hydrogen bonds : bond 0.05424 / 3.22 ( 2038) hydrogen bonds : angle 4.51548 / 3.05 ( 5641) metal coordination : bond 0.00857 / 0.45 ( 8) metal coordination : angle 3.80933 / 1.98 ( 9) Misc. bond : bond 0.00196 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 351 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8878 (mm) REVERT: B 68 GLN cc_start: 0.9184 (tp40) cc_final: 0.8610 (tm-30) REVERT: B 83 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7468 (mmt180) REVERT: C 92 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7164 (tmm-80) REVERT: D 55 ARG cc_start: 0.6777 (mtt180) cc_final: 0.6095 (mmt180) REVERT: E 57 GLU cc_start: 0.7968 (tt0) cc_final: 0.7628 (tt0) REVERT: G 46 LYS cc_start: 0.9373 (mmmt) cc_final: 0.8880 (tptt) REVERT: H 70 ASN cc_start: 0.8908 (m-40) cc_final: 0.8451 (m110) REVERT: H 79 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8454 (pp20) REVERT: H 102 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7991 (mmm160) REVERT: H 111 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7686 (mtmt) REVERT: M 764 PHE cc_start: 0.8229 (m-80) cc_final: 0.7946 (m-80) REVERT: M 1053 ASP cc_start: 0.8843 (p0) cc_final: 0.8624 (p0) REVERT: M 1131 ASP cc_start: 0.8837 (t0) cc_final: 0.8408 (t70) REVERT: R 192 ASP cc_start: 0.8451 (p0) cc_final: 0.8095 (t0) REVERT: R 238 MET cc_start: 0.7456 (tpp) cc_final: 0.7103 (tpt) REVERT: R 349 MET cc_start: 0.9203 (mmm) cc_final: 0.8920 (mmm) REVERT: S 278 ARG cc_start: 0.6427 (mmt-90) cc_final: 0.5072 (tpm170) REVERT: T 70 MET cc_start: 0.3492 (OUTLIER) cc_final: 0.2588 (ttm) REVERT: T 76 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6169 (pt) REVERT: T 188 SER cc_start: 0.5587 (p) cc_final: 0.5348 (m) REVERT: U 250 ARG cc_start: 0.1434 (OUTLIER) cc_final: 0.0993 (ptt180) REVERT: U 258 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5616 (t80) REVERT: V 58 CYS cc_start: 0.8097 (t) cc_final: 0.7775 (t) REVERT: V 221 GLU cc_start: 0.8183 (tp30) cc_final: 0.7869 (mm-30) REVERT: V 309 PHE cc_start: 0.7721 (t80) cc_final: 0.7474 (t80) REVERT: V 406 MET cc_start: 0.8953 (tpp) cc_final: 0.8677 (mmm) REVERT: W 255 LEU cc_start: 0.8362 (mt) cc_final: 0.7815 (tp) REVERT: X 146 GLU cc_start: -0.4772 (OUTLIER) cc_final: -0.4981 (pt0) REVERT: X 150 GLU cc_start: 0.2638 (OUTLIER) cc_final: 0.2043 (pt0) REVERT: X 406 MET cc_start: 0.8471 (mmm) cc_final: 0.8174 (mmm) REVERT: X 431 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7826 (mtp180) REVERT: Y 118 THR cc_start: 0.6658 (m) cc_final: 0.6274 (p) REVERT: Y 198 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.4596 (mtmm) REVERT: Y 223 GLN cc_start: 0.5596 (OUTLIER) cc_final: 0.5373 (tt0) REVERT: Y 268 GLU cc_start: 0.3467 (OUTLIER) cc_final: 0.0615 (mm-30) REVERT: Y 456 ILE cc_start: -0.2955 (OUTLIER) cc_final: -0.3466 (tt) outliers start: 202 outliers final: 144 residues processed: 513 average time/residue: 0.2093 time to fit residues: 182.9912 Evaluate side-chains 479 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 322 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1183 LEU Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1347 MET Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain T residue 455 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 250 ARG Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 251 ASP Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 101 ILE Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 269 optimal weight: 0.4980 chunk 111 optimal weight: 40.0000 chunk 248 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 497 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 97 HIS ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 HIS ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 325 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.090712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.075005 restraints weight = 348017.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.076642 restraints weight = 212508.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.077693 restraints weight = 146101.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.078415 restraints weight = 110426.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.078906 restraints weight = 89831.786| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 45882 Z= 0.206 Angle : 0.755 14.439 63565 Z= 0.391 Chirality : 0.046 0.232 7440 Planarity : 0.005 0.058 6874 Dihedral : 23.834 178.386 9073 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.01 % Allowed : 20.39 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.92 (0.12), residues: 4633 helix: 0.31 (0.11), residues: 2187 sheet: -0.43 (0.21), residues: 599 loop : -1.75 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 327 TYR 0.039 0.003 TYR X 462 PHE 0.021 0.002 PHE M 999 TRP 0.031 0.002 TRP M1343 HIS 0.009 0.002 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (45872) covalent geometry : angle 0.75364 / 0.39 (63556) hydrogen bonds : bond 0.05617 / 3.33 ( 2038) hydrogen bonds : angle 4.59485 / 3.10 ( 5641) metal coordination : bond 0.01159 / 0.58 ( 8) metal coordination : angle 4.04164 / 2.10 ( 9) Misc. bond : bond 0.00191 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 348 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 105 GLU cc_start: 0.8409 (pt0) cc_final: 0.8145 (tp30) REVERT: B 68 GLN cc_start: 0.9199 (tp40) cc_final: 0.8657 (tm-30) REVERT: B 83 ARG cc_start: 0.7932 (mmt90) cc_final: 0.7399 (mtt180) REVERT: B 97 GLU cc_start: 0.8555 (tp30) cc_final: 0.8345 (tp30) REVERT: C 37 LEU cc_start: 0.8269 (mm) cc_final: 0.7603 (mt) REVERT: C 59 LYS cc_start: 0.9405 (tptm) cc_final: 0.8801 (tptp) REVERT: E 57 GLU cc_start: 0.7877 (tt0) cc_final: 0.7529 (tt0) REVERT: G 46 LYS cc_start: 0.9386 (mmmt) cc_final: 0.8902 (tptt) REVERT: H 70 ASN cc_start: 0.8884 (m-40) cc_final: 0.8409 (m110) REVERT: H 102 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8183 (mmm160) REVERT: H 111 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7587 (mtmt) REVERT: M 737 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6808 (t80) REVERT: M 1005 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (tt) REVERT: M 1053 ASP cc_start: 0.8845 (p0) cc_final: 0.8630 (p0) REVERT: M 1131 ASP cc_start: 0.9004 (t0) cc_final: 0.8638 (t70) REVERT: R 69 TRP cc_start: 0.6098 (OUTLIER) cc_final: 0.4158 (m100) REVERT: R 226 LEU cc_start: 0.8589 (tp) cc_final: 0.8332 (tp) REVERT: R 238 MET cc_start: 0.7558 (tpp) cc_final: 0.7300 (tpp) REVERT: R 330 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7481 (mt) REVERT: R 349 MET cc_start: 0.9167 (mmm) cc_final: 0.8841 (mmm) REVERT: S 278 ARG cc_start: 0.6588 (mmt-90) cc_final: 0.5111 (tpm170) REVERT: T 31 LYS cc_start: 0.8744 (mttt) cc_final: 0.8192 (mmpt) REVERT: T 70 MET cc_start: 0.3697 (OUTLIER) cc_final: 0.3315 (ttm) REVERT: T 76 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6887 (pt) REVERT: U 250 ARG cc_start: 0.1584 (OUTLIER) cc_final: 0.1180 (ptt180) REVERT: U 258 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.5537 (t80) REVERT: V 58 CYS cc_start: 0.7984 (t) cc_final: 0.7688 (t) REVERT: V 221 GLU cc_start: 0.8162 (tp30) cc_final: 0.7834 (mm-30) REVERT: V 406 MET cc_start: 0.8884 (tpp) cc_final: 0.8592 (mmm) REVERT: W 255 LEU cc_start: 0.8340 (mt) cc_final: 0.7754 (tp) REVERT: X 146 GLU cc_start: -0.4452 (OUTLIER) cc_final: -0.4741 (pt0) REVERT: X 431 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8028 (mtp180) REVERT: Y 117 LEU cc_start: 0.8648 (tp) cc_final: 0.8408 (tt) REVERT: Y 198 LYS cc_start: 0.5168 (OUTLIER) cc_final: 0.4635 (mtmm) REVERT: Y 268 GLU cc_start: 0.3927 (OUTLIER) cc_final: 0.0998 (mm-30) REVERT: Y 456 ILE cc_start: -0.2682 (OUTLIER) cc_final: -0.3138 (tp) outliers start: 200 outliers final: 136 residues processed: 510 average time/residue: 0.2190 time to fit residues: 188.1263 Evaluate side-chains 465 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 315 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1183 LEU Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1347 MET Chi-restraints excluded: chain M residue 1351 CYS Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 69 TRP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain T residue 455 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 250 ARG Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 251 ASP Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 242 HIS Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 295 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 304 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 154 optimal weight: 0.1980 chunk 458 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 200 optimal weight: 0.1980 chunk 75 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M1352 GLN R 359 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Y 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.090975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.075227 restraints weight = 348989.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.076868 restraints weight = 212050.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.077875 restraints weight = 145464.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.078638 restraints weight = 110059.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.079043 restraints weight = 89180.541| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45882 Z= 0.158 Angle : 0.715 12.246 63565 Z= 0.366 Chirality : 0.045 0.237 7440 Planarity : 0.004 0.055 6874 Dihedral : 23.756 179.248 9063 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.21 % Allowed : 21.74 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.74 (0.12), residues: 4633 helix: 0.53 (0.11), residues: 2190 sheet: -0.53 (0.21), residues: 614 loop : -1.70 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 311 TYR 0.035 0.002 TYR C 88 PHE 0.041 0.002 PHE M 764 TRP 0.023 0.001 TRP M1343 HIS 0.009 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (45872) covalent geometry : angle 0.71384 / 0.37 (63556) hydrogen bonds : bond 0.05244 / 3.09 ( 2038) hydrogen bonds : angle 4.46193 / 3.00 ( 5641) metal coordination : bond 0.00764 / 0.39 ( 8) metal coordination : angle 3.61593 / 1.86 ( 9) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 340 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8891 (mm) REVERT: A 105 GLU cc_start: 0.8418 (pt0) cc_final: 0.8102 (tp30) REVERT: B 68 GLN cc_start: 0.9197 (tp40) cc_final: 0.8656 (tm-30) REVERT: B 83 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7458 (mtt180) REVERT: C 59 LYS cc_start: 0.9399 (tptm) cc_final: 0.8857 (tptp) REVERT: C 92 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7357 (tmm-80) REVERT: D 53 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7702 (mp0) REVERT: D 55 ARG cc_start: 0.6911 (mtt180) cc_final: 0.6081 (mmt180) REVERT: D 59 LYS cc_start: 0.9350 (pttp) cc_final: 0.8990 (pttm) REVERT: E 57 GLU cc_start: 0.7837 (tt0) cc_final: 0.7522 (tt0) REVERT: G 46 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8904 (tptt) REVERT: H 70 ASN cc_start: 0.8890 (m-40) cc_final: 0.8400 (m110) REVERT: H 102 ARG cc_start: 0.8388 (mmm160) cc_final: 0.8156 (mmm160) REVERT: H 111 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7606 (mtmt) REVERT: M 1053 ASP cc_start: 0.8772 (p0) cc_final: 0.8552 (p0) REVERT: M 1131 ASP cc_start: 0.9002 (t0) cc_final: 0.8638 (t70) REVERT: R 192 ASP cc_start: 0.8360 (p0) cc_final: 0.7949 (t0) REVERT: R 226 LEU cc_start: 0.8657 (tp) cc_final: 0.8325 (tp) REVERT: R 238 MET cc_start: 0.7774 (tpp) cc_final: 0.7339 (tpp) REVERT: R 349 MET cc_start: 0.9200 (mmm) cc_final: 0.8944 (mmm) REVERT: S 278 ARG cc_start: 0.6571 (mmt-90) cc_final: 0.5092 (tpm170) REVERT: T 31 LYS cc_start: 0.8661 (mttt) cc_final: 0.8175 (mmpt) REVERT: T 70 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.3606 (ttm) REVERT: T 76 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7216 (pt) REVERT: T 216 ASP cc_start: 0.6277 (t0) cc_final: 0.5878 (p0) REVERT: U 250 ARG cc_start: 0.1433 (OUTLIER) cc_final: 0.1055 (ptt180) REVERT: U 258 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6162 (t80) REVERT: V 58 CYS cc_start: 0.8060 (t) cc_final: 0.7738 (t) REVERT: V 221 GLU cc_start: 0.8102 (tp30) cc_final: 0.7766 (mm-30) REVERT: V 406 MET cc_start: 0.8832 (tpp) cc_final: 0.8574 (mmm) REVERT: W 255 LEU cc_start: 0.8360 (mt) cc_final: 0.7775 (tp) REVERT: X 146 GLU cc_start: -0.4791 (OUTLIER) cc_final: -0.5077 (pt0) REVERT: X 344 MET cc_start: 0.0114 (mmp) cc_final: -0.1832 (tpp) REVERT: X 431 ARG cc_start: 0.8544 (mtt180) cc_final: 0.8188 (mtp180) REVERT: Y 198 LYS cc_start: 0.5162 (OUTLIER) cc_final: 0.4700 (mtmm) REVERT: Y 268 GLU cc_start: 0.4333 (OUTLIER) cc_final: 0.1035 (mm-30) REVERT: Y 323 MET cc_start: 0.8786 (tpp) cc_final: 0.8502 (tpp) REVERT: Y 456 ILE cc_start: -0.2995 (OUTLIER) cc_final: -0.3476 (tp) outliers start: 168 outliers final: 133 residues processed: 479 average time/residue: 0.1859 time to fit residues: 149.7844 Evaluate side-chains 469 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 325 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1347 MET Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 167 ILE Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 250 ARG Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 251 ASP Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 165 HIS Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 242 HIS Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 227 optimal weight: 6.9990 chunk 485 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 450 optimal weight: 0.0030 chunk 435 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 480 optimal weight: 9.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS M 808 GLN M1173 ASN M1263 HIS M1285 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 HIS ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 124 ASN X 357 HIS ** X 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.080404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.066120 restraints weight = 326003.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.067609 restraints weight = 196757.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.068579 restraints weight = 134998.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.069250 restraints weight = 101894.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.069648 restraints weight = 82779.491| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.8008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 45882 Z= 0.291 Angle : 0.910 16.078 63565 Z= 0.470 Chirality : 0.050 0.248 7440 Planarity : 0.006 0.086 6874 Dihedral : 23.934 177.370 9061 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 4.51 % Allowed : 21.99 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.43 (0.12), residues: 4633 helix: -0.11 (0.11), residues: 2191 sheet: -0.75 (0.21), residues: 591 loop : -1.99 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG X 342 TYR 0.029 0.003 TYR C 88 PHE 0.037 0.003 PHE X 125 TRP 0.032 0.003 TRP Y 280 HIS 0.012 0.003 HIS U 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.29 (45872) covalent geometry : angle 0.90825 / 0.47 (63556) hydrogen bonds : bond 0.07207 / 4.32 ( 2038) hydrogen bonds : angle 5.09512 / 3.43 ( 5641) metal coordination : bond 0.01683 / 0.84 ( 8) metal coordination : angle 5.11037 / 2.73 ( 9) Misc. bond : bond 0.00209 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 315 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLN cc_start: 0.9339 (tp40) cc_final: 0.8691 (tm-30) REVERT: B 83 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7526 (mtt-85) REVERT: C 58 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9280 (tm) REVERT: D 53 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7757 (mp0) REVERT: E 57 GLU cc_start: 0.7969 (tt0) cc_final: 0.7581 (tt0) REVERT: G 46 LYS cc_start: 0.9447 (mmmt) cc_final: 0.8984 (tptt) REVERT: H 70 ASN cc_start: 0.9000 (m-40) cc_final: 0.8477 (m110) REVERT: H 79 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8481 (pp20) REVERT: H 102 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8179 (mmm160) REVERT: H 111 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7661 (mtmt) REVERT: M 737 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7066 (t80) REVERT: M 821 MET cc_start: 0.5860 (ptt) cc_final: 0.5455 (ptp) REVERT: M 1053 ASP cc_start: 0.8822 (p0) cc_final: 0.8618 (p0) REVERT: M 1290 MET cc_start: 0.7144 (ptp) cc_final: 0.6723 (ptp) REVERT: M 1314 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5906 (mt) REVERT: R 69 TRP cc_start: 0.6524 (OUTLIER) cc_final: 0.4627 (m100) REVERT: R 238 MET cc_start: 0.7788 (tpp) cc_final: 0.7333 (tpp) REVERT: R 349 MET cc_start: 0.9278 (mmm) cc_final: 0.7944 (mmt) REVERT: S 278 ARG cc_start: 0.6910 (mmt-90) cc_final: 0.5128 (tpm170) REVERT: T 31 LYS cc_start: 0.8762 (mttt) cc_final: 0.8383 (mmpt) REVERT: T 302 GLU cc_start: 0.7843 (tt0) cc_final: 0.7430 (pp20) REVERT: U 250 ARG cc_start: 0.1725 (OUTLIER) cc_final: 0.1408 (ptt180) REVERT: U 258 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7622 (t80) REVERT: V 70 MET cc_start: 0.7618 (tpp) cc_final: 0.7317 (tpp) REVERT: W 29 LEU cc_start: 0.7982 (tp) cc_final: 0.7670 (tp) REVERT: W 255 LEU cc_start: 0.8635 (mt) cc_final: 0.7944 (tp) REVERT: W 323 MET cc_start: 0.8194 (mmp) cc_final: 0.7925 (mmm) REVERT: X 53 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7264 (tm-30) REVERT: X 146 GLU cc_start: -0.4352 (OUTLIER) cc_final: -0.4661 (pt0) REVERT: X 315 MET cc_start: 0.2289 (ptm) cc_final: 0.1951 (ptm) REVERT: X 344 MET cc_start: 0.1753 (mmp) cc_final: -0.0222 (tpp) REVERT: X 431 ARG cc_start: 0.8674 (mtt180) cc_final: 0.8455 (mtp180) REVERT: Y 268 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5455 (pt0) REVERT: Y 314 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7726 (pm20) REVERT: Y 456 ILE cc_start: -0.2864 (OUTLIER) cc_final: -0.3896 (tp) outliers start: 180 outliers final: 135 residues processed: 465 average time/residue: 0.1667 time to fit residues: 131.5627 Evaluate side-chains 440 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 295 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1183 LEU Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1314 ILE Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1343 TRP Chi-restraints excluded: chain M residue 1351 CYS Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 TRP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 134 LYS Chi-restraints excluded: chain T residue 167 ILE Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 455 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 250 ARG Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 293 LEU Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 165 HIS Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 383 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 242 HIS Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 145 optimal weight: 9.9990 chunk 418 optimal weight: 4.9990 chunk 310 optimal weight: 0.0870 chunk 183 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 314 optimal weight: 0.0070 chunk 253 optimal weight: 7.9990 chunk 263 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 0.0770 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.089236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.073585 restraints weight = 348660.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.075207 restraints weight = 209418.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.076215 restraints weight = 142881.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.076958 restraints weight = 107662.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.077465 restraints weight = 87283.746| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.7823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 45882 Z= 0.145 Angle : 0.742 13.117 63565 Z= 0.377 Chirality : 0.045 0.284 7440 Planarity : 0.004 0.061 6874 Dihedral : 23.768 179.482 9057 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.86 % Allowed : 23.75 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.87 (0.12), residues: 4633 helix: 0.44 (0.11), residues: 2185 sheet: -0.68 (0.21), residues: 607 loop : -1.76 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 311 TYR 0.060 0.002 TYR D 88 PHE 0.027 0.002 PHE X 125 TRP 0.020 0.002 TRP M1343 HIS 0.008 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (45872) covalent geometry : angle 0.74001 / 0.38 (63556) hydrogen bonds : bond 0.05328 / 3.13 ( 2038) hydrogen bonds : angle 4.50671 / 3.03 ( 5641) metal coordination : bond 0.00769 / 0.40 ( 8) metal coordination : angle 4.07169 / 2.08 ( 9) Misc. bond : bond 0.00053 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 344 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8888 (mm) REVERT: A 105 GLU cc_start: 0.8394 (pt0) cc_final: 0.8088 (tp30) REVERT: B 68 GLN cc_start: 0.9233 (tp40) cc_final: 0.8676 (tm-30) REVERT: B 83 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7528 (mtt180) REVERT: C 59 LYS cc_start: 0.9398 (tptm) cc_final: 0.8780 (tptp) REVERT: C 92 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7355 (tmm-80) REVERT: D 55 ARG cc_start: 0.6850 (mtt180) cc_final: 0.6566 (mmt90) REVERT: D 59 LYS cc_start: 0.9295 (pttp) cc_final: 0.8824 (pttm) REVERT: E 57 GLU cc_start: 0.7967 (tt0) cc_final: 0.7656 (tt0) REVERT: F 114 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7579 (tm-30) REVERT: G 46 LYS cc_start: 0.9376 (mmmt) cc_final: 0.8928 (tptt) REVERT: H 70 ASN cc_start: 0.8918 (m-40) cc_final: 0.8413 (m110) REVERT: H 79 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8413 (pp20) REVERT: H 108 GLU cc_start: 0.7237 (tp30) cc_final: 0.6764 (tm-30) REVERT: M 737 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.6775 (t80) REVERT: M 821 MET cc_start: 0.5508 (ptt) cc_final: 0.5125 (ptp) REVERT: M 1131 ASP cc_start: 0.9114 (t0) cc_final: 0.8757 (t0) REVERT: M 1290 MET cc_start: 0.6875 (ptp) cc_final: 0.6351 (ptp) REVERT: M 1314 ILE cc_start: 0.5677 (OUTLIER) cc_final: 0.5425 (mt) REVERT: M 1347 MET cc_start: 0.7824 (pmm) cc_final: 0.7359 (pmm) REVERT: R 192 ASP cc_start: 0.8320 (p0) cc_final: 0.7811 (t0) REVERT: R 238 MET cc_start: 0.8052 (tpp) cc_final: 0.7293 (mmm) REVERT: R 349 MET cc_start: 0.9227 (mmm) cc_final: 0.9000 (mmm) REVERT: S 278 ARG cc_start: 0.6745 (mmt-90) cc_final: 0.5113 (tpm170) REVERT: T 31 LYS cc_start: 0.8694 (mttt) cc_final: 0.8314 (mmpt) REVERT: T 159 TYR cc_start: 0.4705 (m-80) cc_final: 0.4374 (m-80) REVERT: T 216 ASP cc_start: 0.6392 (t0) cc_final: 0.6033 (p0) REVERT: T 302 GLU cc_start: 0.7448 (tt0) cc_final: 0.7229 (pp20) REVERT: U 250 ARG cc_start: 0.1421 (OUTLIER) cc_final: 0.1058 (ptt180) REVERT: U 258 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7444 (t80) REVERT: V 70 MET cc_start: 0.7420 (tpp) cc_final: 0.7194 (tpp) REVERT: V 251 ASP cc_start: 0.8299 (m-30) cc_final: 0.8050 (m-30) REVERT: V 315 MET cc_start: 0.8435 (tpt) cc_final: 0.7793 (mmt) REVERT: V 456 LEU cc_start: 0.8766 (pp) cc_final: 0.8351 (tp) REVERT: W 29 LEU cc_start: 0.7769 (tp) cc_final: 0.7552 (tp) REVERT: W 183 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7399 (mmtm) REVERT: W 255 LEU cc_start: 0.8347 (mt) cc_final: 0.7799 (tp) REVERT: X 53 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7108 (tm-30) REVERT: X 146 GLU cc_start: -0.4394 (OUTLIER) cc_final: -0.4712 (pt0) REVERT: X 236 GLU cc_start: 0.7169 (pm20) cc_final: 0.6959 (pm20) REVERT: X 315 MET cc_start: 0.2186 (ptm) cc_final: 0.1952 (ptm) REVERT: X 338 LEU cc_start: 0.8561 (tt) cc_final: 0.8184 (tt) REVERT: X 344 MET cc_start: 0.2250 (mmp) cc_final: 0.0111 (tpp) REVERT: Y 51 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7341 (mtp180) REVERT: Y 213 ASP cc_start: 0.4431 (OUTLIER) cc_final: 0.4197 (p0) REVERT: Y 268 GLU cc_start: 0.5188 (OUTLIER) cc_final: 0.2188 (mm-30) REVERT: Y 314 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7638 (pm20) REVERT: Y 323 MET cc_start: 0.8657 (tpp) cc_final: 0.8408 (tpp) REVERT: Y 455 GLN cc_start: 0.3789 (mp10) cc_final: 0.1453 (tp40) outliers start: 114 outliers final: 91 residues processed: 441 average time/residue: 0.1661 time to fit residues: 123.6023 Evaluate side-chains 424 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 323 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1314 ILE Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1343 TRP Chi-restraints excluded: chain M residue 1351 CYS Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 250 ARG Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 242 HIS Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 420 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 53 optimal weight: 0.0170 chunk 370 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 chunk 384 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 419 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 139 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1352 GLN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.088369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.072654 restraints weight = 350557.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.074238 restraints weight = 211175.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.075275 restraints weight = 144795.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.076009 restraints weight = 109097.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.076517 restraints weight = 88539.465| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45882 Z= 0.151 Angle : 0.733 16.390 63565 Z= 0.372 Chirality : 0.044 0.244 7440 Planarity : 0.004 0.066 6874 Dihedral : 23.685 175.683 9053 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.11 % Allowed : 23.80 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.81 (0.12), residues: 4633 helix: 0.51 (0.11), residues: 2195 sheet: -0.72 (0.20), residues: 615 loop : -1.73 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 23 TYR 0.037 0.002 TYR C 88 PHE 0.023 0.002 PHE X 125 TRP 0.019 0.001 TRP M1343 HIS 0.011 0.001 HIS W 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (45872) covalent geometry : angle 0.73134 / 0.37 (63556) hydrogen bonds : bond 0.05290 / 3.11 ( 2038) hydrogen bonds : angle 4.47170 / 3.00 ( 5641) metal coordination : bond 0.00706 / 0.37 ( 8) metal coordination : angle 3.78614 / 1.96 ( 9) Misc. bond : bond 0.00042 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10303.63 seconds wall clock time: 176 minutes 42.92 seconds (10602.92 seconds total)