Starting phenix.real_space_refine on Wed Aug 27 02:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gen_4396/08_2025/6gen_4396.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gen_4396/08_2025/6gen_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 { model { file = "/net/cci-nas-00/data/ceres_data/6gen_4396/08_2025/6gen_4396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gen_4396/08_2025/6gen_4396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gen_4396/08_2025/6gen_4396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gen_4396/08_2025/6gen_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.00, per 1000 atoms: 0.18 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: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 5.38 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: 12.72 Time building geometry restraints manager: 4.45 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=" F3 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F3 BEF R 502 " pdb="BE BEF R 502 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 45867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 62887 2.84 - 5.68: 579 5.68 - 8.51: 78 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=" 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 angle pdb=" CA TYR X 462 " pdb=" CB TYR X 462 " pdb=" CG TYR X 462 " ideal model delta sigma weight residual 113.90 122.49 -8.59 1.80e+00 3.09e-01 2.28e+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: 5700 0.045 - 0.090: 1269 0.090 - 0.135: 423 0.135 - 0.180: 37 0.180 - 0.225: 11 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 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.11e+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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 46.500 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.901 45882 Z= 0.640 Angle : 0.793 37.602 63565 Z= 0.438 Chirality : 0.043 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 aren 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 covalent geometry : bond 0.00351 (45872) covalent geometry : angle 0.75482 (63556) hydrogen bonds : bond 0.14567 ( 2038) hydrogen bonds : angle 9.25728 ( 5641) metal coordination : bond 0.37033 ( 8) metal coordination : angle 20.51469 ( 9) Misc. bond : bond 0.89996 ( 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 : 1.412 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: symmetry clash REVERT: A 89 ILE cc_start: 0.4546 (mt) cc_final: 0.4318 (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: 0.8324 (t) REVERT: C 78 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6618 (ttm-80) 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: 0.6651 (tt0) REVERT: F 93 GLU cc_start: 0.8648 (mp0) cc_final: 0.8428 (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: 0.8344 (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: 0.6812 (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: 0.7689 (tp) REVERT: R 230 THR cc_start: 0.7902 (p) cc_final: 0.7674 (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: 0.7783 (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: -0.0106 (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: 0.7106 (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: -0.1005 (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: 0.6982 (tt) REVERT: Y 160 ILE cc_start: 0.8727 (mt) cc_final: 0.8509 (tp) REVERT: Y 268 GLU cc_start: 0.2285 (OUTLIER) cc_final: -0.0625 (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: 0.2638 time to fit residues: 595.4633 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 : 1.305 ------------------------------------------------------------------------------- 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: 8.9990 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: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS E 16 GLN E 42 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN G 112 HIS ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 730 GLN M 782 GLN M 808 GLN M 857 GLN M1070 ASN M1082 ASN M1226 GLN M1249 GLN M1285 HIS R 45 HIS R 61 HIS ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN R 247 ASN R 251 GLN ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN R 384 HIS T 124 ASN ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 263 GLN T 271 GLN T 289 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 153 HIS U 155 GLN U 252 GLN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 455 GLN V 94 GLN V 124 ASN 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 36 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN ** Y 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 230 GLN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 326 ASN Y 408 GLN Y 455 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.090405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.074450 restraints weight = 313112.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.076190 restraints weight = 193613.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.077327 restraints weight = 134105.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.078124 restraints weight = 101587.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.078635 restraints weight = 82688.274| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 45882 Z= 0.286 Angle : 0.907 13.960 63565 Z= 0.473 Chirality : 0.048 0.284 7440 Planarity : 0.007 0.079 6874 Dihedral : 24.091 166.560 9136 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 6.21 % Allowed : 17.41 % Favored : 76.38 % 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 aren not related in a simple way. whole: -2.18 (0.11), residues: 4633 helix: -1.22 (0.10), residues: 2160 sheet: -0.46 (0.20), residues: 630 loop : -1.94 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 38 TYR 0.038 0.003 TYR G 86 PHE 0.047 0.003 PHE M 796 TRP 0.028 0.003 TRP U 280 HIS 0.020 0.002 HIS U 153 Details of bonding type rmsd covalent geometry : bond 0.00618 (45872) covalent geometry : angle 0.90378 (63556) hydrogen bonds : bond 0.06904 ( 2038) hydrogen bonds : angle 5.28366 ( 5641) metal coordination : bond 0.01545 ( 8) metal coordination : angle 6.68022 ( 9) Misc. bond : bond 0.00383 ( 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 746 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 498 time to evaluate : 1.245 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: A 105 GLU cc_start: 0.8356 (pt0) cc_final: 0.8090 (pt0) REVERT: B 68 GLN cc_start: 0.9433 (tp40) cc_final: 0.8762 (tm-30) REVERT: C 88 TYR cc_start: 0.8215 (m-10) cc_final: 0.7278 (m-10) REVERT: E 57 GLU cc_start: 0.8007 (tt0) cc_final: 0.7603 (tt0) REVERT: F 26 PHE cc_start: 0.8497 (m-80) cc_final: 0.8253 (m-80) REVERT: F 93 GLU cc_start: 0.9317 (mp0) cc_final: 0.9071 (mp0) REVERT: G 46 LYS cc_start: 0.9368 (mmmt) cc_final: 0.8948 (tptt) REVERT: H 86 TYR cc_start: 0.6890 (m-10) cc_final: 0.6123 (m-10) REVERT: H 102 ARG cc_start: 0.8345 (mmm160) cc_final: 0.8115 (mmm160) REVERT: H 111 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7814 (mtmt) REVERT: M 1214 MET cc_start: 0.9186 (mtp) cc_final: 0.8971 (mtt) REVERT: R 192 ASP cc_start: 0.8528 (p0) cc_final: 0.8245 (t0) REVERT: R 238 MET cc_start: 0.7405 (tpp) cc_final: 0.6850 (tpt) REVERT: R 349 MET cc_start: 0.9081 (mmm) cc_final: 0.8877 (mmm) REVERT: S 12 THR cc_start: 0.8780 (m) cc_final: 0.8215 (m) REVERT: S 48 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5951 (ttp-110) REVERT: S 278 ARG cc_start: 0.6516 (mmt-90) cc_final: 0.5247 (tpm170) REVERT: T 70 MET cc_start: 0.2406 (mmt) cc_final: 0.2181 (mtt) REVERT: T 133 ILE cc_start: -0.1940 (OUTLIER) cc_final: -0.2390 (mt) REVERT: T 315 MET cc_start: 0.8235 (mmp) cc_final: 0.7983 (mmp) REVERT: U 185 LEU cc_start: 0.8173 (mm) cc_final: 0.7702 (tp) REVERT: V 58 CYS cc_start: 0.7845 (t) cc_final: 0.7573 (t) REVERT: V 111 TYR cc_start: 0.6979 (m-80) cc_final: 0.6753 (m-80) REVERT: V 221 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7394 (mm-30) REVERT: V 266 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8412 (tp) REVERT: V 309 PHE cc_start: 0.7786 (t80) cc_final: 0.7431 (t80) REVERT: V 367 LEU cc_start: 0.8707 (mt) cc_final: 0.8352 (mt) REVERT: V 385 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8411 (pp20) REVERT: W 110 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8041 (tm-30) REVERT: W 245 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8568 (t0) REVERT: W 255 LEU cc_start: 0.8318 (mt) cc_final: 0.7759 (tp) REVERT: X 150 GLU cc_start: 0.2536 (OUTLIER) cc_final: 0.2253 (pt0) REVERT: X 329 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8101 (mp0) REVERT: X 431 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7311 (ptp-110) REVERT: Y 117 LEU cc_start: 0.8359 (tp) cc_final: 0.8044 (tp) REVERT: Y 135 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7354 (tt) REVERT: Y 160 ILE cc_start: 0.9034 (mt) cc_final: 0.8648 (tp) REVERT: Y 198 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.3790 (ttmm) REVERT: Y 456 ILE cc_start: -0.1409 (OUTLIER) cc_final: -0.1863 (tp) outliers start: 248 outliers final: 130 residues processed: 687 average time/residue: 0.2324 time to fit residues: 264.5914 Evaluate side-chains 500 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 360 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 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 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 122 THR 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 734 LEU Chi-restraints excluded: chain M residue 757 LEU Chi-restraints excluded: chain M residue 762 MET Chi-restraints excluded: chain M residue 854 THR 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 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 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1343 TRP 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 308 ASP Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 428 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 48 ARG 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 82 SER Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 109 LEU 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 236 VAL Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain U residue 429 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 103 CYS Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 266 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain V residue 385 GLU Chi-restraints excluded: chain W residue 101 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 238 THR Chi-restraints excluded: chain W residue 245 ASP Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 448 ILE 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 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 243 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 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 71 VAL Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 199 ILE 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 315 ASP 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 402 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 454 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: 2.9990 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 502 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 336 optimal weight: 4.9990 chunk 52 optimal weight: 0.0020 chunk 426 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN E 113 HIS F 42 GLN H 112 HIS M1044 ASN M1070 ASN M1302 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1360 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 GLN R 422 HIS S 106 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN U 237 HIS U 272 GLN U 360 ASN V 29 HIS V 190 GLN V 245 GLN V 256 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 205 ASN ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Y 23 HIS Y 252 GLN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 326 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.094872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.079166 restraints weight = 346757.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.080784 restraints weight = 212169.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.081862 restraints weight = 146467.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.082596 restraints weight = 110774.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.083091 restraints weight = 90038.962| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 45882 Z= 0.175 Angle : 0.698 11.638 63565 Z= 0.361 Chirality : 0.043 0.206 7440 Planarity : 0.005 0.052 6874 Dihedral : 23.914 167.921 9088 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.19 % Allowed : 19.26 % Favored : 75.55 % 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 aren not related in a simple way. whole: -1.30 (0.11), residues: 4633 helix: -0.16 (0.10), residues: 2152 sheet: -0.31 (0.21), residues: 587 loop : -1.81 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG V 342 TYR 0.033 0.002 TYR G 86 PHE 0.028 0.002 PHE M 999 TRP 0.021 0.002 TRP U 280 HIS 0.010 0.001 HIS M 827 Details of bonding type rmsd covalent geometry : bond 0.00385 (45872) covalent geometry : angle 0.69552 (63556) hydrogen bonds : bond 0.05170 ( 2038) hydrogen bonds : angle 4.68139 ( 5641) metal coordination : bond 0.00721 ( 8) metal coordination : angle 5.40292 ( 9) Misc. bond : bond 0.00108 ( 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 614 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 407 time to evaluate : 1.444 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: B 68 GLN cc_start: 0.9350 (tp40) cc_final: 0.8620 (tm-30) REVERT: B 83 ARG cc_start: 0.7826 (mmt180) cc_final: 0.6999 (mmt180) REVERT: C 88 TYR cc_start: 0.8204 (m-10) cc_final: 0.7725 (m-10) REVERT: E 57 GLU cc_start: 0.7987 (tt0) cc_final: 0.7540 (tt0) REVERT: F 26 PHE cc_start: 0.8526 (m-80) cc_final: 0.8271 (m-80) REVERT: F 93 GLU cc_start: 0.9288 (mp0) cc_final: 0.8895 (mp0) REVERT: G 46 LYS cc_start: 0.9389 (mmmt) cc_final: 0.8862 (tptt) REVERT: G 75 ARG cc_start: 0.9091 (mmp80) cc_final: 0.8812 (tpp80) REVERT: H 70 ASN cc_start: 0.8859 (m-40) cc_final: 0.8590 (m-40) REVERT: H 102 ARG cc_start: 0.8275 (mmm160) cc_final: 0.8052 (mmm160) REVERT: M 1005 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7906 (tt) REVERT: M 1131 ASP cc_start: 0.8568 (t0) cc_final: 0.8271 (t70) REVERT: M 1326 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7258 (tp) REVERT: M 1347 MET cc_start: 0.6764 (mtm) cc_final: 0.6101 (mtm) REVERT: R 192 ASP cc_start: 0.8491 (p0) cc_final: 0.8154 (t0) REVERT: R 238 MET cc_start: 0.7512 (tpp) cc_final: 0.6968 (tpt) REVERT: R 349 MET cc_start: 0.9079 (mmm) cc_final: 0.7902 (mmt) REVERT: S 55 ASP cc_start: 0.7990 (m-30) cc_final: 0.7033 (m-30) REVERT: S 266 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.7664 (m) REVERT: S 278 ARG cc_start: 0.6517 (mmt-90) cc_final: 0.5043 (tpm170) REVERT: T 70 MET cc_start: 0.2618 (mmt) cc_final: 0.2048 (ttm) REVERT: T 133 ILE cc_start: -0.0794 (OUTLIER) cc_final: -0.1306 (mm) REVERT: T 188 SER cc_start: 0.5371 (p) cc_final: 0.5125 (m) REVERT: U 24 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8540 (p) REVERT: U 44 MET cc_start: 0.7155 (mmm) cc_final: 0.6894 (mmm) REVERT: U 62 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: U 185 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7778 (tp) REVERT: U 258 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5276 (t80) REVERT: V 58 CYS cc_start: 0.8106 (t) cc_final: 0.7751 (t) REVERT: V 105 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8198 (tt) REVERT: V 309 PHE cc_start: 0.7762 (t80) cc_final: 0.7444 (t80) REVERT: V 367 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8278 (mt) REVERT: W 110 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7783 (tm-30) REVERT: W 169 TYR cc_start: 0.7464 (m-10) cc_final: 0.7204 (m-10) REVERT: W 206 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6449 (p90) REVERT: W 255 LEU cc_start: 0.8363 (mt) cc_final: 0.7813 (tp) REVERT: X 85 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8211 (mtpt) REVERT: X 431 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7794 (mtp180) REVERT: Y 117 LEU cc_start: 0.8430 (tp) cc_final: 0.8085 (tp) REVERT: Y 118 THR cc_start: 0.6680 (m) cc_final: 0.6211 (p) REVERT: Y 135 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7201 (tp) REVERT: Y 160 ILE cc_start: 0.9062 (mt) cc_final: 0.8768 (tp) REVERT: Y 268 GLU cc_start: 0.3529 (OUTLIER) cc_final: 0.0297 (mm-30) outliers start: 207 outliers final: 108 residues processed: 574 average time/residue: 0.2215 time to fit residues: 214.2536 Evaluate side-chains 458 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 336 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 112 ILE 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 70 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 104 ILE 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 M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 773 VAL Chi-restraints excluded: chain M residue 871 MET 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 1152 TYR Chi-restraints excluded: chain M residue 1204 SER 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 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 R residue 369 LEU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 236 VAL 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 259 THR Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 300 MET 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 105 LEU Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 209 VAL 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 145 ILE Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 206 PHE Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 85 LYS 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 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 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 101 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 215 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 90 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 386 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 409 optimal weight: 3.9990 chunk 428 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.092276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.076481 restraints weight = 349604.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.078127 restraints weight = 212376.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.079183 restraints weight = 146502.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.079898 restraints weight = 110854.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.080362 restraints weight = 90247.835| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 45882 Z= 0.181 Angle : 0.699 13.031 63565 Z= 0.361 Chirality : 0.043 0.265 7440 Planarity : 0.004 0.046 6874 Dihedral : 23.664 169.507 9074 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.41 % Allowed : 19.51 % Favored : 75.08 % 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 aren not related in a simple way. whole: -0.92 (0.12), residues: 4633 helix: 0.25 (0.11), residues: 2195 sheet: -0.34 (0.21), residues: 601 loop : -1.72 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 59 TYR 0.043 0.002 TYR G 86 PHE 0.037 0.002 PHE Y 221 TRP 0.015 0.002 TRP Y 280 HIS 0.008 0.001 HIS U 153 Details of bonding type rmsd covalent geometry : bond 0.00394 (45872) covalent geometry : angle 0.69751 (63556) hydrogen bonds : bond 0.05304 ( 2038) hydrogen bonds : angle 4.46457 ( 5641) metal coordination : bond 0.01015 ( 8) metal coordination : angle 4.18348 ( 9) Misc. bond : bond 0.00043 ( 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 593 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 377 time to evaluate : 1.226 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: B 68 GLN cc_start: 0.9354 (tp40) cc_final: 0.8653 (tm-30) REVERT: B 83 ARG cc_start: 0.8040 (mmt180) cc_final: 0.7405 (mtt-85) REVERT: C 88 TYR cc_start: 0.8383 (m-10) cc_final: 0.7282 (m-10) REVERT: E 57 GLU cc_start: 0.7997 (tt0) cc_final: 0.7546 (tt0) REVERT: F 26 PHE cc_start: 0.8482 (m-80) cc_final: 0.8118 (m-80) REVERT: G 34 LYS cc_start: 0.5299 (OUTLIER) cc_final: 0.4025 (pttp) REVERT: G 46 LYS cc_start: 0.9410 (mmmt) cc_final: 0.8890 (tptt) REVERT: G 75 ARG cc_start: 0.9099 (mmp80) cc_final: 0.8865 (tpp80) REVERT: H 70 ASN cc_start: 0.8835 (m-40) cc_final: 0.8557 (m-40) REVERT: H 86 TYR cc_start: 0.7120 (m-10) cc_final: 0.5894 (m-10) REVERT: H 102 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8039 (mmm160) REVERT: M 820 TYR cc_start: 0.6730 (m-10) cc_final: 0.6528 (m-10) REVERT: M 1053 ASP cc_start: 0.8870 (p0) cc_final: 0.8609 (p0) REVERT: M 1214 MET cc_start: 0.9118 (mtt) cc_final: 0.8813 (mtt) REVERT: M 1347 MET cc_start: 0.7082 (mtm) cc_final: 0.6728 (mtm) REVERT: R 69 TRP cc_start: 0.6353 (OUTLIER) cc_final: 0.4362 (m100) REVERT: R 192 ASP cc_start: 0.8572 (p0) cc_final: 0.8134 (t0) REVERT: R 226 LEU cc_start: 0.8712 (tp) cc_final: 0.8454 (tp) REVERT: R 238 MET cc_start: 0.7664 (tpp) cc_final: 0.7107 (tpt) REVERT: R 349 MET cc_start: 0.9152 (mmm) cc_final: 0.7983 (mmt) REVERT: S 278 ARG cc_start: 0.6596 (mmt-90) cc_final: 0.4971 (tpm170) REVERT: T 31 LYS cc_start: 0.8845 (mttt) cc_final: 0.8257 (mmpt) REVERT: U 62 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: U 142 GLU cc_start: 0.5107 (mm-30) cc_final: 0.4882 (mm-30) REVERT: U 185 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8115 (tp) REVERT: U 258 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6380 (t80) REVERT: V 58 CYS cc_start: 0.8222 (t) cc_final: 0.7886 (t) REVERT: V 251 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7846 (t0) REVERT: V 309 PHE cc_start: 0.7858 (t80) cc_final: 0.7540 (t80) REVERT: W 110 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7787 (tm-30) REVERT: W 169 TYR cc_start: 0.7576 (m-10) cc_final: 0.7223 (m-10) REVERT: W 255 LEU cc_start: 0.8439 (mt) cc_final: 0.7753 (tp) REVERT: X 85 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8515 (mtpt) REVERT: X 122 MET cc_start: 0.3916 (ptp) cc_final: 0.3697 (mpp) REVERT: X 146 GLU cc_start: -0.4705 (OUTLIER) cc_final: -0.4964 (pt0) REVERT: X 316 LEU cc_start: 0.6118 (mt) cc_final: 0.5837 (mt) REVERT: X 323 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: X 431 ARG cc_start: 0.8444 (mtt180) cc_final: 0.8050 (mtp180) REVERT: Y 117 LEU cc_start: 0.8486 (tp) cc_final: 0.8121 (tp) REVERT: Y 118 THR cc_start: 0.7108 (m) cc_final: 0.6569 (p) REVERT: Y 160 ILE cc_start: 0.9117 (mt) cc_final: 0.8816 (tp) REVERT: Y 198 LYS cc_start: 0.5235 (OUTLIER) cc_final: 0.4411 (ttmm) REVERT: Y 268 GLU cc_start: 0.3905 (OUTLIER) cc_final: 0.1065 (mm-30) REVERT: Y 456 ILE cc_start: -0.2625 (OUTLIER) cc_final: -0.3086 (tt) outliers start: 216 outliers final: 137 residues processed: 548 average time/residue: 0.2145 time to fit residues: 197.7428 Evaluate side-chains 480 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 331 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 89 ILE 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 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 93 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 104 ILE 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 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 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 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain M residue 1204 SER Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR 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 135 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 8 ILE 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 109 GLU Chi-restraints excluded: chain T residue 136 THR 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 62 GLN Chi-restraints excluded: chain U residue 95 ASP 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 173 ASN Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 236 VAL 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 273 ILE 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 115 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 264 ASP Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 247 ILE 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 282 GLU Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 403 ILE 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 85 LYS 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 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 323 TYR 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 92 LEU Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 215 MET 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 454 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: 9.9990 chunk 264 optimal weight: 0.9990 chunk 328 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 365 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 337 optimal weight: 0.9980 chunk 394 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS F 42 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1070 ASN M1352 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 HIS ** R 289 ASN ** 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 289 ASN T 461 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS ** W 36 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.089082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.073490 restraints weight = 348049.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.075120 restraints weight = 211475.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.076177 restraints weight = 145213.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.076870 restraints weight = 109370.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.077314 restraints weight = 88994.313| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.7295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 45882 Z= 0.199 Angle : 0.726 16.519 63565 Z= 0.375 Chirality : 0.043 0.360 7440 Planarity : 0.005 0.096 6874 Dihedral : 23.638 165.832 9066 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.36 % Allowed : 21.27 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.12), residues: 4633 helix: 0.44 (0.11), residues: 2183 sheet: -0.48 (0.21), residues: 603 loop : -1.73 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 78 TYR 0.051 0.002 TYR G 86 PHE 0.018 0.002 PHE X 125 TRP 0.021 0.002 TRP Y 280 HIS 0.009 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00432 (45872) covalent geometry : angle 0.72407 (63556) hydrogen bonds : bond 0.05345 ( 2038) hydrogen bonds : angle 4.53850 ( 5641) metal coordination : bond 0.00884 ( 8) metal coordination : angle 4.30998 ( 9) Misc. bond : bond 0.00060 ( 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 578 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 364 time to evaluate : 1.556 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 81 ASP cc_start: 0.6413 (t0) cc_final: 0.6190 (p0) REVERT: A 105 GLU cc_start: 0.8464 (pt0) cc_final: 0.8160 (tp30) REVERT: B 68 GLN cc_start: 0.9317 (tp40) cc_final: 0.8648 (tm-30) REVERT: B 83 ARG cc_start: 0.7896 (mmt180) cc_final: 0.7263 (mtt-85) REVERT: E 57 GLU cc_start: 0.8076 (tt0) cc_final: 0.7658 (tt0) REVERT: F 26 PHE cc_start: 0.8336 (m-80) cc_final: 0.7762 (m-80) REVERT: F 93 GLU cc_start: 0.9227 (mp0) cc_final: 0.8929 (mp0) REVERT: G 46 LYS cc_start: 0.9386 (mmmt) cc_final: 0.8888 (tptt) REVERT: G 75 ARG cc_start: 0.9025 (mmp80) cc_final: 0.8771 (tpp80) REVERT: G 104 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (mt) REVERT: H 70 ASN cc_start: 0.8878 (m-40) cc_final: 0.8552 (m110) REVERT: H 102 ARG cc_start: 0.8445 (mmm160) cc_final: 0.7807 (mmp80) REVERT: M 737 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6727 (t80) REVERT: M 1053 ASP cc_start: 0.8838 (p0) cc_final: 0.8601 (p0) REVERT: M 1347 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5048 (mtm) REVERT: M 1386 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6995 (tmtt) REVERT: R 69 TRP cc_start: 0.6127 (OUTLIER) cc_final: 0.4212 (m100) REVERT: R 238 MET cc_start: 0.7875 (tpp) cc_final: 0.7416 (tpp) REVERT: R 349 MET cc_start: 0.9066 (mmm) cc_final: 0.7941 (mmt) REVERT: S 278 ARG cc_start: 0.6822 (mmt-90) cc_final: 0.5078 (tpm170) REVERT: T 31 LYS cc_start: 0.8673 (mttt) cc_final: 0.8280 (mmpt) REVERT: T 70 MET cc_start: 0.4057 (OUTLIER) cc_final: 0.3822 (mmt) REVERT: T 76 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7190 (pt) REVERT: T 216 ASP cc_start: 0.6434 (t0) cc_final: 0.6029 (p0) REVERT: T 302 GLU cc_start: 0.7652 (tt0) cc_final: 0.7312 (pp20) REVERT: U 20 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8090 (pp) REVERT: U 62 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: U 154 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6414 (pttt) REVERT: U 185 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8138 (tp) REVERT: U 258 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7082 (t80) REVERT: U 322 MET cc_start: 0.8612 (ppp) cc_final: 0.8347 (ppp) REVERT: V 58 CYS cc_start: 0.7959 (t) cc_final: 0.7661 (t) REVERT: V 309 PHE cc_start: 0.7718 (t80) cc_final: 0.7435 (t80) REVERT: W 29 LEU cc_start: 0.7917 (tp) cc_final: 0.7633 (tp) REVERT: W 255 LEU cc_start: 0.8539 (mt) cc_final: 0.7895 (tp) REVERT: X 85 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (mtmt) REVERT: X 122 MET cc_start: 0.3908 (ptp) cc_final: 0.3375 (ptp) REVERT: X 146 GLU cc_start: -0.4547 (OUTLIER) cc_final: -0.4943 (pt0) REVERT: X 315 MET cc_start: 0.1645 (ptm) cc_final: 0.0397 (mmp) REVERT: X 323 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: X 394 GLN cc_start: 0.5567 (tm-30) cc_final: 0.5282 (tm-30) REVERT: X 431 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8345 (mtp180) REVERT: Y 27 THR cc_start: 0.7811 (p) cc_final: 0.7581 (p) REVERT: Y 51 ARG cc_start: 0.8288 (mtm180) cc_final: 0.6910 (ttp-170) REVERT: Y 160 ILE cc_start: 0.9223 (mt) cc_final: 0.8958 (tp) REVERT: Y 198 LYS cc_start: 0.5236 (OUTLIER) cc_final: 0.4291 (ttmm) REVERT: Y 268 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.1973 (mm-30) REVERT: Y 456 ILE cc_start: -0.2449 (OUTLIER) cc_final: -0.3032 (tp) outliers start: 214 outliers final: 143 residues processed: 533 average time/residue: 0.2257 time to fit residues: 201.2775 Evaluate side-chains 489 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 328 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 43 VAL 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 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 50 ILE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 108 VAL 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 97 ILE Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU 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 937 VAL Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 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 1285 HIS 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 1386 LYS 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 135 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 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 136 THR 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 T residue 461 ASN Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP 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 128 LYS Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 154 LYS 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 236 VAL 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 259 THR Chi-restraints excluded: chain U residue 273 ILE 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 103 CYS Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 247 ILE Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 293 LEU 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 403 ILE 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 85 LYS 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 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 323 TYR 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 14 LEU Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER 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 268 GLU 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 411 MET Chi-restraints excluded: chain Y residue 420 VAL 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: 5.9990 chunk 232 optimal weight: 10.0000 chunk 440 optimal weight: 5.9990 chunk 368 optimal weight: 0.0030 chunk 87 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 410 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 483 optimal weight: 0.7980 chunk 312 optimal weight: 7.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN M1082 ASN M1263 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.072660 restraints weight = 350494.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.074234 restraints weight = 210699.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.075260 restraints weight = 144405.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.075981 restraints weight = 108525.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.076401 restraints weight = 88074.858| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 45882 Z= 0.175 Angle : 0.690 9.932 63565 Z= 0.355 Chirality : 0.042 0.245 7440 Planarity : 0.004 0.062 6874 Dihedral : 23.500 166.783 9063 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 4.91 % Allowed : 22.65 % Favored : 72.44 % 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 aren not related in a simple way. whole: -0.67 (0.12), residues: 4633 helix: 0.62 (0.11), residues: 2190 sheet: -0.43 (0.21), residues: 587 loop : -1.74 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 204 TYR 0.029 0.002 TYR D 88 PHE 0.024 0.002 PHE X 125 TRP 0.041 0.002 TRP M1343 HIS 0.005 0.001 HIS U 153 Details of bonding type rmsd covalent geometry : bond 0.00384 (45872) covalent geometry : angle 0.68838 (63556) hydrogen bonds : bond 0.05123 ( 2038) hydrogen bonds : angle 4.38306 ( 5641) metal coordination : bond 0.00801 ( 8) metal coordination : angle 4.16590 ( 9) Misc. bond : bond 0.00063 ( 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 555 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 359 time to evaluate : 1.195 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: B 68 GLN cc_start: 0.9304 (tp40) cc_final: 0.8631 (tm-30) REVERT: B 83 ARG cc_start: 0.7807 (mmt180) cc_final: 0.7184 (mtt-85) REVERT: C 37 LEU cc_start: 0.8345 (mm) cc_final: 0.7748 (mt) REVERT: D 55 ARG cc_start: 0.6716 (mtt180) cc_final: 0.6024 (mmt180) REVERT: D 79 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8139 (ptmt) REVERT: E 57 GLU cc_start: 0.8017 (tt0) cc_final: 0.7604 (tt0) REVERT: F 24 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7037 (tp) REVERT: F 26 PHE cc_start: 0.8292 (m-80) cc_final: 0.7619 (m-80) REVERT: F 93 GLU cc_start: 0.9166 (mp0) cc_final: 0.8914 (mp0) REVERT: G 46 LYS cc_start: 0.9413 (mmmt) cc_final: 0.8967 (tptt) REVERT: G 75 ARG cc_start: 0.8951 (mmp80) cc_final: 0.8722 (tpp80) REVERT: H 70 ASN cc_start: 0.8862 (m-40) cc_final: 0.8515 (m110) REVERT: H 102 ARG cc_start: 0.8464 (mmm160) cc_final: 0.8109 (mmm160) REVERT: H 108 GLU cc_start: 0.7988 (tp30) cc_final: 0.7368 (tm-30) REVERT: M 737 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.6823 (t80) REVERT: M 821 MET cc_start: 0.5503 (ptt) cc_final: 0.5078 (ptp) REVERT: M 1053 ASP cc_start: 0.8828 (p0) cc_final: 0.8572 (p0) REVERT: M 1214 MET cc_start: 0.8663 (mtt) cc_final: 0.8380 (mtt) REVERT: R 69 TRP cc_start: 0.6169 (OUTLIER) cc_final: 0.4206 (m100) REVERT: R 238 MET cc_start: 0.8017 (tpp) cc_final: 0.7346 (tpp) REVERT: R 349 MET cc_start: 0.9073 (mmm) cc_final: 0.8000 (mmt) REVERT: S 103 MET cc_start: 0.8327 (tpt) cc_final: 0.8064 (ttt) REVERT: S 278 ARG cc_start: 0.6840 (mmt-90) cc_final: 0.5084 (tpm170) REVERT: T 31 LYS cc_start: 0.8819 (mttt) cc_final: 0.8420 (mmpt) REVERT: T 70 MET cc_start: 0.3858 (OUTLIER) cc_final: 0.3641 (ptt) REVERT: T 76 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7688 (pt) REVERT: T 216 ASP cc_start: 0.6465 (t0) cc_final: 0.6189 (p0) REVERT: T 302 GLU cc_start: 0.7815 (tt0) cc_final: 0.7541 (pp20) REVERT: U 62 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: U 185 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8272 (tp) REVERT: U 252 GLN cc_start: 0.3436 (OUTLIER) cc_final: 0.2906 (pt0) REVERT: U 258 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7009 (t80) REVERT: U 349 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8479 (t0) REVERT: V 58 CYS cc_start: 0.7963 (t) cc_final: 0.7642 (t) REVERT: W 29 LEU cc_start: 0.7876 (tp) cc_final: 0.7614 (tp) REVERT: W 169 TYR cc_start: 0.7249 (m-10) cc_final: 0.6994 (m-10) REVERT: W 255 LEU cc_start: 0.8673 (mt) cc_final: 0.7933 (tp) REVERT: X 53 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7123 (tm-30) REVERT: X 61 ILE cc_start: 0.9184 (mt) cc_final: 0.8849 (mm) REVERT: X 122 MET cc_start: 0.3887 (ptp) cc_final: 0.3461 (ptp) REVERT: X 146 GLU cc_start: -0.4571 (OUTLIER) cc_final: -0.4855 (pt0) REVERT: X 315 MET cc_start: 0.1959 (ptm) cc_final: 0.1287 (mmm) REVERT: X 323 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6225 (m-80) REVERT: X 344 MET cc_start: 0.1375 (mmp) cc_final: -0.0859 (tpp) REVERT: Y 27 THR cc_start: 0.7758 (p) cc_final: 0.7458 (p) REVERT: Y 51 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7616 (mtp180) REVERT: Y 160 ILE cc_start: 0.9201 (mt) cc_final: 0.8947 (tp) REVERT: Y 198 LYS cc_start: 0.5509 (OUTLIER) cc_final: 0.4586 (ttmm) REVERT: Y 268 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5177 (pt0) REVERT: Y 314 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7717 (pm20) REVERT: Y 456 ILE cc_start: -0.2662 (OUTLIER) cc_final: -0.3359 (tp) outliers start: 196 outliers final: 138 residues processed: 513 average time/residue: 0.2239 time to fit residues: 192.7419 Evaluate side-chains 478 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 325 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 118 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 30 THR 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 50 ILE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 109 LEU 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 937 VAL 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 1075 VAL Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL 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 1276 ASP Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR 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 R residue 287 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 64 LEU 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 230 VAL 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 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP 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 144 GLN 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 236 VAL Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 349 ASP Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 247 ILE Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 258 PHE Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 282 GLU 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 367 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 115 VAL 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 323 TYR 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 433 GLU Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 101 ILE Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 202 LEU 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 359 TYR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 454 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: 0.8980 chunk 111 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 497 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 322 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1352 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 325 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.087785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.072214 restraints weight = 349107.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.073806 restraints weight = 209913.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.074851 restraints weight = 143099.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.075450 restraints weight = 107538.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.076011 restraints weight = 88154.753| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45882 Z= 0.157 Angle : 0.680 13.703 63565 Z= 0.347 Chirality : 0.042 0.331 7440 Planarity : 0.004 0.062 6874 Dihedral : 23.412 168.508 9059 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.76 % Allowed : 22.82 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.12), residues: 4633 helix: 0.71 (0.11), residues: 2195 sheet: -0.50 (0.21), residues: 588 loop : -1.69 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 204 TYR 0.034 0.002 TYR G 86 PHE 0.036 0.002 PHE T 309 TRP 0.016 0.001 TRP M1343 HIS 0.005 0.001 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00345 (45872) covalent geometry : angle 0.67825 (63556) hydrogen bonds : bond 0.04945 ( 2038) hydrogen bonds : angle 4.31269 ( 5641) metal coordination : bond 0.00572 ( 8) metal coordination : angle 3.70746 ( 9) Misc. bond : bond 0.00055 ( 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 537 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 347 time to evaluate : 1.091 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: A 105 GLU cc_start: 0.8368 (pt0) cc_final: 0.8122 (tp30) REVERT: B 68 GLN cc_start: 0.9309 (tp40) cc_final: 0.8636 (tm-30) REVERT: B 83 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7173 (mtt-85) REVERT: C 37 LEU cc_start: 0.8339 (mm) cc_final: 0.7736 (mt) REVERT: D 46 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8489 (tt) REVERT: D 53 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7744 (mp0) REVERT: D 79 LYS cc_start: 0.8275 (mmtm) cc_final: 0.8057 (tttt) REVERT: E 57 GLU cc_start: 0.8000 (tt0) cc_final: 0.7583 (tt0) REVERT: F 24 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.5491 (tp) REVERT: F 26 PHE cc_start: 0.8245 (m-80) cc_final: 0.7811 (m-80) REVERT: G 46 LYS cc_start: 0.9398 (mmmt) cc_final: 0.8993 (tptt) REVERT: H 70 ASN cc_start: 0.8892 (m-40) cc_final: 0.8554 (m110) REVERT: H 102 ARG cc_start: 0.8477 (mmm160) cc_final: 0.8110 (mmm160) REVERT: M 737 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.6783 (t80) REVERT: M 829 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8889 (mp) REVERT: R 69 TRP cc_start: 0.6258 (OUTLIER) cc_final: 0.4314 (m100) REVERT: R 238 MET cc_start: 0.8385 (tpp) cc_final: 0.8010 (tpp) REVERT: R 253 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6955 (tp) REVERT: R 349 MET cc_start: 0.9036 (mmm) cc_final: 0.7977 (mmt) REVERT: S 103 MET cc_start: 0.8303 (tpt) cc_final: 0.8045 (ttt) REVERT: S 278 ARG cc_start: 0.6963 (mmt-90) cc_final: 0.5105 (tpm170) REVERT: T 31 LYS cc_start: 0.8815 (mttt) cc_final: 0.8546 (mmtt) REVERT: T 76 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7849 (pt) REVERT: T 216 ASP cc_start: 0.6624 (t0) cc_final: 0.6351 (p0) REVERT: T 232 LEU cc_start: 0.7187 (tt) cc_final: 0.6463 (mm) REVERT: U 62 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: U 165 MET cc_start: 0.6923 (mmt) cc_final: 0.6717 (mmm) REVERT: U 185 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8355 (tp) REVERT: U 252 GLN cc_start: 0.3427 (OUTLIER) cc_final: 0.3074 (pt0) REVERT: U 258 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6962 (t80) REVERT: U 349 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8427 (t0) REVERT: V 58 CYS cc_start: 0.8052 (t) cc_final: 0.7737 (t) REVERT: V 456 LEU cc_start: 0.8803 (pp) cc_final: 0.8380 (tp) REVERT: W 29 LEU cc_start: 0.7820 (tp) cc_final: 0.7592 (tp) REVERT: W 169 TYR cc_start: 0.7281 (m-10) cc_final: 0.7012 (m-10) REVERT: W 255 LEU cc_start: 0.8717 (mt) cc_final: 0.7929 (tp) REVERT: W 352 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6574 (mt) REVERT: X 53 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7137 (tm-30) REVERT: X 146 GLU cc_start: -0.4466 (OUTLIER) cc_final: -0.4781 (pt0) REVERT: X 315 MET cc_start: 0.2249 (ptm) cc_final: 0.2022 (mmm) REVERT: X 323 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: X 344 MET cc_start: 0.2706 (mmp) cc_final: 0.0792 (tpp) REVERT: X 387 ARG cc_start: 0.7700 (tpt170) cc_final: 0.7477 (mmm160) REVERT: Y 27 THR cc_start: 0.8060 (p) cc_final: 0.7785 (p) REVERT: Y 160 ILE cc_start: 0.9298 (mt) cc_final: 0.9068 (tp) REVERT: Y 198 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4848 (mtmm) REVERT: Y 199 ILE cc_start: -0.0963 (OUTLIER) cc_final: -0.1182 (mp) REVERT: Y 268 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5595 (pt0) REVERT: Y 314 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7859 (pm20) REVERT: Y 456 ILE cc_start: -0.2673 (OUTLIER) cc_final: -0.3417 (tp) outliers start: 190 outliers final: 131 residues processed: 499 average time/residue: 0.1887 time to fit residues: 160.2195 Evaluate side-chains 461 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 311 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 118 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 30 THR 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 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 43 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ILE 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 109 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 829 ILE Chi-restraints excluded: chain M residue 937 VAL 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 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 1276 ASP Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR 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 135 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain S residue 1 MET 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 S residue 244 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 136 THR 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 291 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP 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 173 ASN Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 349 ASP Chi-restraints excluded: chain V residue 70 MET Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 222 PHE Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 247 ILE Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 258 PHE Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 293 LEU Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 121 LEU 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 323 TYR 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 X residue 439 VAL Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 101 ILE Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 202 LEU 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 359 TYR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 411 MET 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: 1.9990 chunk 310 optimal weight: 0.0010 chunk 177 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 458 optimal weight: 0.0000 chunk 359 optimal weight: 0.0270 chunk 248 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 200 optimal weight: 0.0370 chunk 75 optimal weight: 6.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN F 42 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 325 ASN ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 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 = 0.4295 r_free = 0.4295 target = 0.089705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.074275 restraints weight = 345925.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.075878 restraints weight = 207267.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.076920 restraints weight = 141524.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.077612 restraints weight = 106673.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.078110 restraints weight = 86640.617| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 45882 Z= 0.127 Angle : 0.661 13.002 63565 Z= 0.333 Chirality : 0.041 0.205 7440 Planarity : 0.004 0.063 6874 Dihedral : 23.262 165.923 9058 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.13 % Allowed : 24.82 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.12), residues: 4633 helix: 0.89 (0.11), residues: 2186 sheet: -0.53 (0.21), residues: 595 loop : -1.66 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M1210 TYR 0.040 0.001 TYR D 72 PHE 0.017 0.001 PHE X 125 TRP 0.017 0.001 TRP M1343 HIS 0.006 0.001 HIS U 242 Details of bonding type rmsd covalent geometry : bond 0.00275 (45872) covalent geometry : angle 0.66009 (63556) hydrogen bonds : bond 0.04649 ( 2038) hydrogen bonds : angle 4.08009 ( 5641) metal coordination : bond 0.00320 ( 8) metal coordination : angle 3.26366 ( 9) Misc. bond : bond 0.00018 ( 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 479 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 354 time to evaluate : 0.994 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: A 105 GLU cc_start: 0.8341 (pt0) cc_final: 0.8088 (tp30) REVERT: B 68 GLN cc_start: 0.9305 (tp40) cc_final: 0.8652 (tm-30) REVERT: B 83 ARG cc_start: 0.7770 (mmt180) cc_final: 0.7216 (mtt-85) REVERT: C 37 LEU cc_start: 0.8225 (mm) cc_final: 0.7634 (mt) REVERT: E 57 GLU cc_start: 0.7966 (tt0) cc_final: 0.7597 (tt0) REVERT: F 26 PHE cc_start: 0.8225 (m-80) cc_final: 0.7990 (m-80) REVERT: F 114 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7469 (tm-30) REVERT: G 46 LYS cc_start: 0.9367 (mmmt) cc_final: 0.8978 (tptt) REVERT: H 70 ASN cc_start: 0.8859 (m-40) cc_final: 0.8525 (m110) REVERT: H 102 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8074 (mmm160) REVERT: M 737 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6737 (t80) REVERT: M 1326 LEU cc_start: 0.7890 (tp) cc_final: 0.7482 (tp) REVERT: R 238 MET cc_start: 0.8316 (tpp) cc_final: 0.7371 (tpp) REVERT: R 349 MET cc_start: 0.9005 (mmm) cc_final: 0.7871 (mmt) REVERT: R 400 MET cc_start: 0.7650 (mmm) cc_final: 0.6858 (mmt) REVERT: S 103 MET cc_start: 0.8275 (tpt) cc_final: 0.8045 (ttt) REVERT: S 278 ARG cc_start: 0.7001 (mmt-90) cc_final: 0.5186 (tpm170) REVERT: T 31 LYS cc_start: 0.8832 (mttt) cc_final: 0.8538 (mmtt) REVERT: T 76 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8025 (pt) REVERT: U 62 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: U 115 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: U 165 MET cc_start: 0.6964 (mmt) cc_final: 0.6736 (mmm) REVERT: U 185 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8368 (tp) REVERT: U 258 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6874 (t80) REVERT: V 58 CYS cc_start: 0.8100 (t) cc_final: 0.7769 (t) REVERT: V 251 ASP cc_start: 0.8469 (m-30) cc_final: 0.8202 (m-30) REVERT: V 456 LEU cc_start: 0.8909 (pp) cc_final: 0.8504 (tp) REVERT: W 29 LEU cc_start: 0.7824 (tp) cc_final: 0.7603 (tp) REVERT: W 169 TYR cc_start: 0.7427 (m-10) cc_final: 0.7112 (m-10) REVERT: W 255 LEU cc_start: 0.8625 (mt) cc_final: 0.7907 (tp) REVERT: X 53 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7069 (tm-30) REVERT: X 61 ILE cc_start: 0.9174 (mt) cc_final: 0.8836 (mm) REVERT: X 116 LYS cc_start: 0.4246 (pttt) cc_final: 0.3729 (tptm) REVERT: X 146 GLU cc_start: -0.4627 (OUTLIER) cc_final: -0.4934 (pt0) REVERT: X 315 MET cc_start: 0.2202 (ptm) cc_final: 0.1843 (mmm) REVERT: X 323 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: X 338 LEU cc_start: 0.8664 (tt) cc_final: 0.8309 (tt) REVERT: Y 27 THR cc_start: 0.8043 (p) cc_final: 0.7783 (p) REVERT: Y 160 ILE cc_start: 0.9318 (mt) cc_final: 0.9111 (tp) REVERT: Y 198 LYS cc_start: 0.5262 (OUTLIER) cc_final: 0.4784 (mtmm) REVERT: Y 215 MET cc_start: 0.7258 (pmm) cc_final: 0.6597 (mpp) REVERT: Y 268 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5265 (pt0) REVERT: Y 314 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7684 (pm20) REVERT: Y 456 ILE cc_start: -0.2250 (OUTLIER) cc_final: -0.3022 (tp) outliers start: 125 outliers final: 90 residues processed: 455 average time/residue: 0.1839 time to fit residues: 140.7353 Evaluate side-chains 416 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 315 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 43 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 97 ILE 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 M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1316 VAL 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 201 ILE Chi-restraints excluded: chain R residue 287 VAL 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 76 LEU Chi-restraints excluded: chain T residue 82 SER 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 U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 115 GLU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 272 GLN Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain V residue 70 MET Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 190 ILE Chi-restraints excluded: chain W residue 258 PHE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 115 VAL 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 323 TYR 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 439 VAL Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU 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 411 MET Chi-restraints excluded: chain Y residue 454 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: 5.9990 chunk 485 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 450 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 286 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 797 HIS M1173 ASN ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 HIS ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 238 HIS ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.083975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.068478 restraints weight = 349471.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.070023 restraints weight = 209644.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.070976 restraints weight = 142995.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.071642 restraints weight = 108640.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.072005 restraints weight = 88750.257| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 45882 Z= 0.246 Angle : 0.802 14.125 63565 Z= 0.414 Chirality : 0.045 0.451 7440 Planarity : 0.006 0.068 6874 Dihedral : 23.476 172.499 9052 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.91 % Allowed : 24.50 % Favored : 71.59 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.12), residues: 4633 helix: 0.46 (0.11), residues: 2195 sheet: -0.77 (0.21), residues: 595 loop : -1.87 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Y 204 TYR 0.038 0.003 TYR D 88 PHE 0.031 0.002 PHE X 125 TRP 0.026 0.002 TRP M1343 HIS 0.010 0.002 HIS X 29 Details of bonding type rmsd covalent geometry : bond 0.00537 (45872) covalent geometry : angle 0.80010 (63556) hydrogen bonds : bond 0.06159 ( 2038) hydrogen bonds : angle 4.67190 ( 5641) metal coordination : bond 0.01427 ( 8) metal coordination : angle 4.37604 ( 9) Misc. bond : bond 0.00101 ( 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 465 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 309 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: A 81 ASP cc_start: 0.6450 (m-30) cc_final: 0.6167 (p0) REVERT: B 68 GLN cc_start: 0.9321 (tp40) cc_final: 0.8717 (tm-30) REVERT: B 83 ARG cc_start: 0.7831 (mmt180) cc_final: 0.7190 (mtt-85) REVERT: E 57 GLU cc_start: 0.8012 (tt0) cc_final: 0.7635 (tt0) REVERT: F 26 PHE cc_start: 0.8280 (m-80) cc_final: 0.7973 (m-80) REVERT: F 96 LYS cc_start: 0.9054 (tppt) cc_final: 0.8829 (tppt) REVERT: G 46 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9008 (tptt) REVERT: H 70 ASN cc_start: 0.9055 (m-40) cc_final: 0.8733 (m-40) REVERT: H 102 ARG cc_start: 0.8528 (mmm160) cc_final: 0.7728 (mmp80) REVERT: M 737 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.6962 (t80) REVERT: M 777 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: M 829 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8922 (mp) REVERT: R 69 TRP cc_start: 0.6476 (OUTLIER) cc_final: 0.4713 (m100) REVERT: R 238 MET cc_start: 0.8277 (tpp) cc_final: 0.7846 (mmm) REVERT: R 253 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7194 (tp) REVERT: R 349 MET cc_start: 0.9043 (mmm) cc_final: 0.7941 (mmt) REVERT: R 400 MET cc_start: 0.7762 (mmm) cc_final: 0.7043 (mmt) REVERT: S 103 MET cc_start: 0.8334 (tpt) cc_final: 0.8055 (ttt) REVERT: S 278 ARG cc_start: 0.7202 (mmt-90) cc_final: 0.5330 (tpm170) REVERT: T 31 LYS cc_start: 0.8950 (mttt) cc_final: 0.8750 (mmtt) REVERT: T 76 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8154 (pt) REVERT: T 232 LEU cc_start: 0.7736 (tt) cc_final: 0.7254 (mm) REVERT: T 246 ASP cc_start: 0.7514 (t0) cc_final: 0.6761 (t0) REVERT: U 62 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: U 252 GLN cc_start: 0.2744 (OUTLIER) cc_final: 0.2488 (pt0) REVERT: U 258 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7327 (t80) REVERT: U 349 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8474 (t0) REVERT: V 58 CYS cc_start: 0.8129 (t) cc_final: 0.7857 (t) REVERT: V 456 LEU cc_start: 0.8927 (pp) cc_final: 0.8517 (tp) REVERT: W 29 LEU cc_start: 0.8031 (tp) cc_final: 0.7820 (tp) REVERT: W 169 TYR cc_start: 0.7540 (m-10) cc_final: 0.7201 (m-10) REVERT: X 53 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7365 (pm20) REVERT: X 116 LYS cc_start: 0.4607 (pttt) cc_final: 0.4187 (tttm) REVERT: X 146 GLU cc_start: -0.4148 (OUTLIER) cc_final: -0.4479 (pt0) REVERT: X 323 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: X 387 ARG cc_start: 0.7643 (tpt170) cc_final: 0.7437 (mmm160) REVERT: Y 198 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5147 (mtmm) REVERT: Y 215 MET cc_start: 0.7505 (pmm) cc_final: 0.7224 (pmm) REVERT: Y 268 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6896 (pt0) REVERT: Y 314 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8194 (pm20) REVERT: Y 456 ILE cc_start: -0.2278 (OUTLIER) cc_final: -0.3617 (tp) outliers start: 156 outliers final: 108 residues processed: 438 average time/residue: 0.1662 time to fit residues: 122.9605 Evaluate side-chains 405 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 282 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU 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 30 THR Chi-restraints excluded: chain C residue 43 VAL 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 43 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 109 LEU 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 737 TYR Chi-restraints excluded: chain M residue 777 TYR Chi-restraints excluded: chain M residue 829 ILE Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR 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 135 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 216 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP 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 128 LYS Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 252 GLN 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 321 VAL Chi-restraints excluded: chain U residue 349 ASP Chi-restraints excluded: chain V residue 70 MET Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 222 PHE Chi-restraints excluded: chain V residue 267 SER Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 247 ILE Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 258 PHE 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 305 CYS Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 133 ILE 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 323 TYR 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 439 VAL Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 101 ILE Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER 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: 10.0000 chunk 418 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 213 optimal weight: 0.4980 chunk 314 optimal weight: 0.7980 chunk 253 optimal weight: 8.9990 chunk 263 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 299 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.086306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.070886 restraints weight = 348172.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.072470 restraints weight = 207450.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.073481 restraints weight = 140910.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.074169 restraints weight = 105966.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.074543 restraints weight = 85896.134| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.9031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45882 Z= 0.143 Angle : 0.709 14.049 63565 Z= 0.358 Chirality : 0.042 0.316 7440 Planarity : 0.004 0.062 6874 Dihedral : 23.376 169.501 9044 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.58 % Allowed : 26.13 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.12), residues: 4633 helix: 0.74 (0.11), residues: 2189 sheet: -0.61 (0.21), residues: 589 loop : -1.72 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 126 TYR 0.044 0.002 TYR G 86 PHE 0.029 0.001 PHE X 125 TRP 0.017 0.001 TRP M1343 HIS 0.005 0.001 HIS U 242 Details of bonding type rmsd covalent geometry : bond 0.00317 (45872) covalent geometry : angle 0.70772 (63556) hydrogen bonds : bond 0.04892 ( 2038) hydrogen bonds : angle 4.32104 ( 5641) metal coordination : bond 0.00443 ( 8) metal coordination : angle 3.52191 ( 9) Misc. bond : bond 0.00040 ( 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 426 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 323 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8358 (pt0) cc_final: 0.8115 (tp30) REVERT: B 68 GLN cc_start: 0.9243 (tp40) cc_final: 0.8711 (tm-30) REVERT: B 83 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7206 (mtt-85) REVERT: C 37 LEU cc_start: 0.8327 (mm) cc_final: 0.7716 (mt) REVERT: E 57 GLU cc_start: 0.7952 (tt0) cc_final: 0.7591 (tt0) REVERT: F 26 PHE cc_start: 0.8212 (m-80) cc_final: 0.7902 (m-80) REVERT: F 114 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7491 (tm-30) REVERT: G 46 LYS cc_start: 0.9357 (mmmt) cc_final: 0.9002 (tptt) REVERT: H 70 ASN cc_start: 0.8927 (m-40) cc_final: 0.8576 (m110) REVERT: H 102 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8109 (mmm160) REVERT: M 737 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6892 (t80) REVERT: M 829 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8865 (mp) REVERT: M 1039 ASP cc_start: 0.7409 (t0) cc_final: 0.7180 (t70) REVERT: R 238 MET cc_start: 0.8411 (tpp) cc_final: 0.7793 (tpp) REVERT: R 286 TYR cc_start: 0.7855 (p90) cc_final: 0.7448 (p90) REVERT: R 349 MET cc_start: 0.9017 (mmm) cc_final: 0.7905 (mmt) REVERT: R 400 MET cc_start: 0.7704 (mmm) cc_final: 0.7005 (mmt) REVERT: S 103 MET cc_start: 0.8314 (tpt) cc_final: 0.8041 (ttt) REVERT: S 278 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.5214 (tpm170) REVERT: T 31 LYS cc_start: 0.8930 (mttt) cc_final: 0.8710 (mmtt) REVERT: T 232 LEU cc_start: 0.7623 (tt) cc_final: 0.7140 (mt) REVERT: T 246 ASP cc_start: 0.7334 (t0) cc_final: 0.6626 (t0) REVERT: T 315 MET cc_start: 0.8505 (mmm) cc_final: 0.8288 (mmm) REVERT: U 62 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: U 165 MET cc_start: 0.6792 (mmt) cc_final: 0.6518 (mmm) REVERT: U 185 LEU cc_start: 0.8913 (mm) cc_final: 0.8481 (tp) REVERT: U 258 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7182 (t80) REVERT: V 58 CYS cc_start: 0.8114 (t) cc_final: 0.7768 (t) REVERT: V 456 LEU cc_start: 0.8928 (pp) cc_final: 0.8566 (tp) REVERT: W 29 LEU cc_start: 0.7912 (tp) cc_final: 0.7711 (tp) REVERT: W 169 TYR cc_start: 0.7486 (m-10) cc_final: 0.7139 (m-10) REVERT: W 255 LEU cc_start: 0.8820 (mt) cc_final: 0.7979 (tp) REVERT: W 323 MET cc_start: 0.7965 (mmm) cc_final: 0.7720 (mmm) REVERT: X 53 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7293 (tm-30) REVERT: X 116 LYS cc_start: 0.4434 (pttt) cc_final: 0.4138 (tttm) REVERT: X 146 GLU cc_start: -0.4176 (OUTLIER) cc_final: -0.4509 (pt0) REVERT: X 323 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: X 387 ARG cc_start: 0.7623 (tpt170) cc_final: 0.7382 (mmm160) REVERT: Y 198 LYS cc_start: 0.5557 (OUTLIER) cc_final: 0.4694 (ttmm) REVERT: Y 215 MET cc_start: 0.7293 (pmm) cc_final: 0.6567 (mpp) REVERT: Y 268 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6703 (pt0) REVERT: Y 314 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7900 (pm20) REVERT: Y 455 GLN cc_start: 0.4622 (mp10) cc_final: 0.1613 (tp40) REVERT: Y 456 ILE cc_start: -0.2490 (OUTLIER) cc_final: -0.2977 (tp) outliers start: 103 outliers final: 85 residues processed: 407 average time/residue: 0.1664 time to fit residues: 114.0738 Evaluate side-chains 396 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 302 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU 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 58 LEU Chi-restraints excluded: chain C residue 68 ASP 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 43 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 829 ILE Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1280 GLN Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR 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 201 ILE Chi-restraints excluded: chain R residue 287 VAL 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 S residue 244 CYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP 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 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain V residue 70 MET Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 369 ILE Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 258 PHE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 113 VAL Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 133 ILE 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 284 LEU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 323 TYR 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 439 VAL Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 101 ILE Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER 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 53 optimal weight: 0.6980 chunk 370 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 384 optimal weight: 6.9990 chunk 276 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 238 HIS ** V 341 ASN ** 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.083523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.068207 restraints weight = 351029.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.069714 restraints weight = 208998.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.070693 restraints weight = 143054.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.071374 restraints weight = 107363.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.071743 restraints weight = 86915.416| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.9545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 45882 Z= 0.204 Angle : 0.760 13.498 63565 Z= 0.388 Chirality : 0.044 0.443 7440 Planarity : 0.005 0.119 6874 Dihedral : 23.418 173.856 9044 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.91 % Allowed : 26.05 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.12), residues: 4633 helix: 0.61 (0.11), residues: 2199 sheet: -0.77 (0.20), residues: 605 loop : -1.84 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Y 204 TYR 0.045 0.002 TYR G 86 PHE 0.032 0.002 PHE X 125 TRP 0.022 0.002 TRP M1343 HIS 0.006 0.001 HIS U 242 Details of bonding type rmsd covalent geometry : bond 0.00450 (45872) covalent geometry : angle 0.75822 (63556) hydrogen bonds : bond 0.05497 ( 2038) hydrogen bonds : angle 4.54930 ( 5641) metal coordination : bond 0.01119 ( 8) metal coordination : angle 3.89528 ( 9) Misc. bond : bond 0.00077 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10060.23 seconds wall clock time: 172 minutes 19.60 seconds (10339.60 seconds total)