Starting phenix.real_space_refine on Sun Feb 18 06:39:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c01_16349/02_2024/8c01_16349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c01_16349/02_2024/8c01_16349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c01_16349/02_2024/8c01_16349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c01_16349/02_2024/8c01_16349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c01_16349/02_2024/8c01_16349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c01_16349/02_2024/8c01_16349.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1545 5.49 5 S 93 5.16 5 C 39828 2.51 5 N 13249 2.21 5 O 17969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72685 Number of models: 1 Model: "" Number of chains: 32 Chain: "2" Number of atoms: 32971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1545, 32971 Classifications: {'RNA': 1545} Modifications used: {'rna2p_pur': 137, 'rna2p_pyr': 94, 'rna3p_pur': 698, 'rna3p_pyr': 616} Link IDs: {'rna2p': 231, 'rna3p': 1313} Chain breaks: 30 Chain: "B" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1588 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 476 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain breaks: 1 Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 118} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1009 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1096 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "K" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 471 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "P" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1590 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "Q" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "R" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1557 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Chain breaks: 1 Chain: "S" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "T" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "V" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 1 Chain: "W" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "X" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1137 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "Z" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 926 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 673 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1046 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "e" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 883 Classifications: {'peptide': 200} Incomplete info: {'backbone_only': 178} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 7 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 245 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 376 Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 300 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "o" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2503 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain breaks: 3 Chain: "p" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1425 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain: "r" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1818 Classifications: {'peptide': 239} Incomplete info: {'backbone_only': 35} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain breaks: 8 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "t" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4813 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 29, 'TRANS': 568} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 63583 SG CYS o 304 130.968 144.232 171.886 1.00 64.56 S ATOM 63604 SG CYS o 307 129.454 144.132 175.248 1.00 68.23 S ATOM 63738 SG CYS o 323 129.685 140.947 173.210 1.00 47.78 S ATOM 63755 SG CYS o 326 127.099 143.546 172.304 1.00 64.96 S Time building chain proxies: 28.85, per 1000 atoms: 0.40 Number of scatterers: 72685 At special positions: 0 Unit cell: (206.184, 259.424, 214.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 93 16.00 P 1545 15.00 O 17969 8.00 N 13249 7.00 C 39828 6.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.50 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN o1000 " pdb="ZN ZN o1000 " - pdb=" SG CYS o 307 " pdb="ZN ZN o1000 " - pdb=" SG CYS o 323 " pdb="ZN ZN o1000 " - pdb=" SG CYS o 304 " pdb="ZN ZN o1000 " - pdb=" SG CYS o 326 " Number of angles added : 6 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9144 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 49 sheets defined 42.1% alpha, 17.6% beta 472 base pairs and 811 stacking pairs defined. Time for finding SS restraints: 22.01 Creating SS restraints... Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 55 through 62 removed outlier: 3.525A pdb=" N VAL B 59 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP B 60 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 62 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.694A pdb=" N SER B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.602A pdb=" N ASP B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.518A pdb=" N VAL B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 183 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.596A pdb=" N LYS B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.268A pdb=" N GLU C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.964A pdb=" N ASN C 97 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 51 through 66 removed outlier: 3.825A pdb=" N GLY E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.557A pdb=" N SER E 120 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 41 through 44 Processing helix chain 'F' and resid 45 through 54 Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.674A pdb=" N SER F 61 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 97 removed outlier: 3.549A pdb=" N ARG F 82 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN F 83 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.614A pdb=" N LYS F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 117 Processing helix chain 'H' and resid 27 through 32 Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 39 through 50 Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'H' and resid 62 through 74 removed outlier: 4.710A pdb=" N ARG H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.514A pdb=" N ILE H 119 " --> pdb=" O ARG H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 131 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 10 through 26 removed outlier: 5.047A pdb=" N ASN I 16 " --> pdb=" O GLN I 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 97 through 111 removed outlier: 4.064A pdb=" N ASN I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS I 103 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 111 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 142 Processing helix chain 'K' and resid 43 through 54 removed outlier: 3.535A pdb=" N LYS K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 72 through 86 removed outlier: 3.805A pdb=" N ILE K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 8 Processing helix chain 'P' and resid 10 through 20 Processing helix chain 'P' and resid 49 through 65 Processing helix chain 'P' and resid 69 through 71 No H-bonds generated for 'chain 'P' and resid 69 through 71' Processing helix chain 'P' and resid 79 through 81 No H-bonds generated for 'chain 'P' and resid 79 through 81' Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'P' and resid 129 through 137 Processing helix chain 'P' and resid 166 through 185 Processing helix chain 'P' and resid 198 through 203 Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 57 through 62 Processing helix chain 'Q' and resid 70 through 75 Processing helix chain 'Q' and resid 76 through 80 Processing helix chain 'Q' and resid 106 through 114 removed outlier: 3.507A pdb=" N MET Q 113 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 176 removed outlier: 3.560A pdb=" N LYS Q 174 " --> pdb=" O GLU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 189 Processing helix chain 'Q' and resid 191 through 202 removed outlier: 4.021A pdb=" N LYS Q 195 " --> pdb=" O GLU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 232 removed outlier: 4.146A pdb=" N LEU Q 228 " --> pdb=" O ASP Q 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 47 removed outlier: 3.541A pdb=" N LEU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 59 removed outlier: 4.331A pdb=" N ILE R 56 " --> pdb=" O THR R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 73 removed outlier: 4.237A pdb=" N ILE R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 135 removed outlier: 3.535A pdb=" N ILE R 130 " --> pdb=" O ARG R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 removed outlier: 3.710A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 220 Processing helix chain 'R' and resid 221 through 223 No H-bonds generated for 'chain 'R' and resid 221 through 223' Processing helix chain 'R' and resid 226 through 230 Processing helix chain 'R' and resid 238 through 243 Processing helix chain 'R' and resid 243 through 248 Processing helix chain 'S' and resid 15 through 19 Processing helix chain 'S' and resid 37 through 41 Processing helix chain 'S' and resid 44 through 51 Processing helix chain 'S' and resid 57 through 66 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 247 through 258 Processing helix chain 'T' and resid 20 through 25 Processing helix chain 'T' and resid 39 through 46 removed outlier: 6.518A pdb=" N ASP T 43 " --> pdb=" O ALA T 40 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU T 44 " --> pdb=" O VAL T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 61 No H-bonds generated for 'chain 'T' and resid 59 through 61' Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 180 through 225 removed outlier: 3.551A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 14 through 31 removed outlier: 3.529A pdb=" N LEU U 18 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER U 31 " --> pdb=" O LEU U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 38 Processing helix chain 'U' and resid 52 through 54 No H-bonds generated for 'chain 'U' and resid 52 through 54' Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.738A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.549A pdb=" N LEU U 77 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 116 Processing helix chain 'U' and resid 117 through 130 removed outlier: 3.930A pdb=" N VAL U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 162 Processing helix chain 'U' and resid 165 through 178 Processing helix chain 'V' and resid 25 through 29 removed outlier: 3.655A pdb=" N GLU V 28 " --> pdb=" O ARG V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 51 No H-bonds generated for 'chain 'V' and resid 49 through 51' Processing helix chain 'V' and resid 88 through 94 Processing helix chain 'V' and resid 106 through 118 Processing helix chain 'V' and resid 136 through 147 removed outlier: 3.740A pdb=" N LYS V 142 " --> pdb=" O ASN V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 150 No H-bonds generated for 'chain 'V' and resid 148 through 150' Processing helix chain 'V' and resid 153 through 158 Processing helix chain 'V' and resid 159 through 162 Processing helix chain 'V' and resid 172 through 177 Processing helix chain 'V' and resid 186 through 198 Processing helix chain 'W' and resid 20 through 35 Processing helix chain 'W' and resid 39 through 60 removed outlier: 3.957A pdb=" N ILE W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 83 removed outlier: 3.795A pdb=" N VAL W 83 " --> pdb=" O ARG W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 97 removed outlier: 3.535A pdb=" N VAL W 96 " --> pdb=" O LYS W 92 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 92 through 97' Processing helix chain 'W' and resid 100 through 106 removed outlier: 3.982A pdb=" N PHE W 104 " --> pdb=" O LYS W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 116 removed outlier: 3.771A pdb=" N TYR W 114 " --> pdb=" O GLN W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 131 removed outlier: 3.595A pdb=" N VAL W 127 " --> pdb=" O HIS W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 154 removed outlier: 3.989A pdb=" N LYS W 154 " --> pdb=" O ASP W 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 151 through 154' Processing helix chain 'W' and resid 170 through 185 Processing helix chain 'X' and resid 45 through 51 removed outlier: 3.563A pdb=" N ILE X 49 " --> pdb=" O PRO X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 43 Processing helix chain 'Y' and resid 46 through 58 Processing helix chain 'Y' and resid 62 through 67 Processing helix chain 'Y' and resid 70 through 77 Processing helix chain 'Y' and resid 85 through 105 removed outlier: 3.542A pdb=" N GLU Y 103 " --> pdb=" O ARG Y 99 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG Y 104 " --> pdb=" O LYS Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 132 removed outlier: 3.557A pdb=" N ILE Y 116 " --> pdb=" O LYS Y 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU Y 117 " --> pdb=" O PHE Y 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 151 Processing helix chain 'Z' and resid 43 through 47 Processing helix chain 'Z' and resid 50 through 54 Processing helix chain 'Z' and resid 56 through 75 Processing helix chain 'Z' and resid 95 through 108 removed outlier: 3.541A pdb=" N ALA Z 101 " --> pdb=" O GLY Z 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 62 Processing helix chain 'a' and resid 64 through 76 Processing helix chain 'b' and resid 5 through 21 removed outlier: 3.598A pdb=" N ASP b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 44 Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 85 through 94 Processing helix chain 'b' and resid 113 through 120 Processing helix chain 'c' and resid 11 through 23 Processing helix chain 'c' and resid 26 through 35 removed outlier: 3.529A pdb=" N LYS c 31 " --> pdb=" O ASN c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 40 Processing helix chain 'c' and resid 89 through 96 Processing helix chain 'c' and resid 132 through 137 Processing helix chain 'd' and resid 16 through 18 No H-bonds generated for 'chain 'd' and resid 16 through 18' Processing helix chain 'd' and resid 36 through 48 removed outlier: 3.510A pdb=" N GLU d 42 " --> pdb=" O ASP d 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 53 No H-bonds generated for 'chain 'd' and resid 51 through 53' Processing helix chain 'd' and resid 78 through 86 removed outlier: 3.516A pdb=" N LYS d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 94 Processing helix chain 'd' and resid 104 through 116 Processing helix chain 'd' and resid 122 through 132 removed outlier: 3.899A pdb=" N ALA d 126 " --> pdb=" O GLY d 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS d 127 " --> pdb=" O LYS d 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 222 removed outlier: 4.274A pdb=" N ILE e 220 " --> pdb=" O THR e 216 " (cutoff:3.500A) Processing helix chain 'e' and resid 230 through 236 removed outlier: 3.548A pdb=" N ILE e 236 " --> pdb=" O LEU e 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 237 through 239 No H-bonds generated for 'chain 'e' and resid 237 through 239' Processing helix chain 'e' and resid 241 through 250 removed outlier: 4.875A pdb=" N TYR e 247 " --> pdb=" O GLN e 243 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL e 248 " --> pdb=" O ASP e 244 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR e 249 " --> pdb=" O VAL e 245 " (cutoff:3.500A) Processing helix chain 'e' and resid 251 through 254 Processing helix chain 'e' and resid 255 through 264 removed outlier: 3.686A pdb=" N VAL e 259 " --> pdb=" O SER e 255 " (cutoff:3.500A) Processing helix chain 'e' and resid 274 through 282 Processing helix chain 'e' and resid 282 through 294 Processing helix chain 'e' and resid 300 through 310 Processing helix chain 'e' and resid 313 through 321 Processing helix chain 'e' and resid 332 through 343 removed outlier: 3.533A pdb=" N VAL e 341 " --> pdb=" O ILE e 337 " (cutoff:3.500A) Processing helix chain 'e' and resid 348 through 359 removed outlier: 3.597A pdb=" N ALA e 354 " --> pdb=" O LEU e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 360 through 361 No H-bonds generated for 'chain 'e' and resid 360 through 361' Processing helix chain 'e' and resid 367 through 367 No H-bonds generated for 'chain 'e' and resid 367 through 367' Processing helix chain 'e' and resid 368 through 376 removed outlier: 3.526A pdb=" N ILE e 372 " --> pdb=" O THR e 368 " (cutoff:3.500A) Processing helix chain 'e' and resid 377 through 379 No H-bonds generated for 'chain 'e' and resid 377 through 379' Processing helix chain 'e' and resid 384 through 392 removed outlier: 3.849A pdb=" N TYR e 392 " --> pdb=" O ASP e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 415 through 425 Processing helix chain 'e' and resid 426 through 427 No H-bonds generated for 'chain 'e' and resid 426 through 427' Processing helix chain 'e' and resid 435 through 435 No H-bonds generated for 'chain 'e' and resid 435 through 435' Processing helix chain 'e' and resid 436 through 445 Processing helix chain 'e' and resid 455 through 460 Processing helix chain 'f' and resid 11 through 17 removed outlier: 3.649A pdb=" N ARG f 17 " --> pdb=" O ALA f 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 32 through 45 removed outlier: 3.537A pdb=" N LYS g 36 " --> pdb=" O GLY g 32 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR g 41 " --> pdb=" O ARG g 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 22 removed outlier: 3.649A pdb=" N GLN o 22 " --> pdb=" O PRO o 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 28 removed outlier: 3.536A pdb=" N TYR o 27 " --> pdb=" O SER o 23 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 44 Processing helix chain 'o' and resid 46 through 59 removed outlier: 3.830A pdb=" N LYS o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN o 52 " --> pdb=" O GLN o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 68 through 83 removed outlier: 3.791A pdb=" N PHE o 78 " --> pdb=" O LYS o 74 " (cutoff:3.500A) Processing helix chain 'o' and resid 84 through 87 Processing helix chain 'o' and resid 89 through 107 removed outlier: 4.766A pdb=" N ILE o 104 " --> pdb=" O TYR o 100 " (cutoff:3.500A) Processing helix chain 'o' and resid 228 through 236 Processing helix chain 'o' and resid 271 through 281 removed outlier: 3.547A pdb=" N VAL o 277 " --> pdb=" O ALA o 273 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN o 280 " --> pdb=" O ASN o 276 " (cutoff:3.500A) Processing helix chain 'o' and resid 370 through 378 removed outlier: 4.035A pdb=" N GLY o 378 " --> pdb=" O GLN o 374 " (cutoff:3.500A) Processing helix chain 'o' and resid 397 through 419 removed outlier: 3.523A pdb=" N GLU o 401 " --> pdb=" O GLN o 397 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS o 402 " --> pdb=" O LYS o 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL o 403 " --> pdb=" O GLU o 399 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 124 removed outlier: 4.345A pdb=" N THR p 107 " --> pdb=" O PRO p 103 " (cutoff:3.500A) Proline residue: p 108 - end of helix removed outlier: 5.016A pdb=" N THR p 114 " --> pdb=" O ARG p 110 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS p 115 " --> pdb=" O ASN p 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR p 117 " --> pdb=" O TRP p 113 " (cutoff:3.500A) Proline residue: p 118 - end of helix Processing helix chain 'p' and resid 150 through 165 Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'p' and resid 172 through 177 removed outlier: 3.580A pdb=" N ARG p 176 " --> pdb=" O ILE p 172 " (cutoff:3.500A) Processing helix chain 'p' and resid 188 through 190 No H-bonds generated for 'chain 'p' and resid 188 through 190' Processing helix chain 'p' and resid 195 through 207 Processing helix chain 'p' and resid 210 through 220 Processing helix chain 'p' and resid 236 through 252 removed outlier: 3.521A pdb=" N ARG p 241 " --> pdb=" O PHE p 237 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER p 246 " --> pdb=" O MET p 242 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER p 249 " --> pdb=" O GLU p 245 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU p 250 " --> pdb=" O SER p 246 " (cutoff:3.500A) Processing helix chain 'p' and resid 255 through 272 removed outlier: 3.641A pdb=" N VAL p 259 " --> pdb=" O PRO p 255 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY p 261 " --> pdb=" O GLY p 257 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN p 262 " --> pdb=" O LYS p 258 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.553A pdb=" N LEU r 19 " --> pdb=" O ASP r 15 " (cutoff:3.500A) Processing helix chain 'r' and resid 23 through 26 removed outlier: 3.967A pdb=" N SER r 26 " --> pdb=" O GLU r 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 23 through 26' Processing helix chain 'r' and resid 35 through 40 Processing helix chain 'r' and resid 47 through 57 removed outlier: 3.690A pdb=" N ALA r 52 " --> pdb=" O GLY r 48 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE r 53 " --> pdb=" O THR r 49 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 83 Processing helix chain 'r' and resid 85 through 92 Processing helix chain 'r' and resid 153 through 172 removed outlier: 4.081A pdb=" N LEU r 157 " --> pdb=" O HIS r 153 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS r 172 " --> pdb=" O MET r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 198 through 200 No H-bonds generated for 'chain 'r' and resid 198 through 200' Processing helix chain 'r' and resid 205 through 224 removed outlier: 3.532A pdb=" N ILE r 217 " --> pdb=" O LEU r 213 " (cutoff:3.500A) Processing helix chain 'r' and resid 264 through 283 Processing helix chain 'r' and resid 320 through 325 removed outlier: 4.177A pdb=" N LEU r 324 " --> pdb=" O ASN r 320 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL r 325 " --> pdb=" O LEU r 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 320 through 325' Processing helix chain 't' and resid 50 through 74 removed outlier: 3.501A pdb=" N GLN t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 77 No H-bonds generated for 'chain 't' and resid 75 through 77' Processing helix chain 't' and resid 96 through 107 removed outlier: 4.129A pdb=" N ILE t 100 " --> pdb=" O ASP t 96 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS t 107 " --> pdb=" O LYS t 103 " (cutoff:3.500A) Processing helix chain 't' and resid 108 through 109 No H-bonds generated for 'chain 't' and resid 108 through 109' Processing helix chain 't' and resid 110 through 114 Processing helix chain 't' and resid 129 through 132 Processing helix chain 't' and resid 144 through 153 Processing helix chain 't' and resid 172 through 184 removed outlier: 3.558A pdb=" N LEU t 182 " --> pdb=" O ARG t 178 " (cutoff:3.500A) Processing helix chain 't' and resid 194 through 199 removed outlier: 3.507A pdb=" N VAL t 198 " --> pdb=" O LEU t 195 " (cutoff:3.500A) Processing helix chain 't' and resid 201 through 220 removed outlier: 3.662A pdb=" N VAL t 208 " --> pdb=" O PHE t 204 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE t 219 " --> pdb=" O TYR t 215 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 245 Processing helix chain 't' and resid 250 through 255 Processing helix chain 't' and resid 464 through 482 Processing helix chain 't' and resid 493 through 499 removed outlier: 3.554A pdb=" N ARG t 497 " --> pdb=" O SER t 493 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU t 498 " --> pdb=" O ALA t 494 " (cutoff:3.500A) Processing helix chain 't' and resid 533 through 549 removed outlier: 3.611A pdb=" N ASN t 547 " --> pdb=" O LYS t 543 " (cutoff:3.500A) Processing helix chain 't' and resid 564 through 571 removed outlier: 3.957A pdb=" N GLU t 569 " --> pdb=" O PHE t 566 " (cutoff:3.500A) Processing helix chain 't' and resid 585 through 589 removed outlier: 4.474A pdb=" N HIS t 589 " --> pdb=" O LEU t 586 " (cutoff:3.500A) Processing helix chain 't' and resid 723 through 730 Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 103 Processing sheet with id=AA3, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AA4, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.501A pdb=" N VAL E 76 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TYR E 97 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR E 78 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 6 through 12 removed outlier: 5.928A pdb=" N LEU F 28 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL F 67 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS F 30 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 17 Processing sheet with id=AA7, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.508A pdb=" N LYS I 92 " --> pdb=" O LYS I 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'K' and resid 59 through 60 removed outlier: 7.224A pdb=" N ILE K 100 " --> pdb=" O ILE K 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 40 through 44 removed outlier: 7.093A pdb=" N VAL L 25 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY L 17 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLN L 27 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL L 15 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG L 29 " --> pdb=" O ILE L 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 37 through 40 removed outlier: 6.857A pdb=" N VAL P 47 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 96 through 99 removed outlier: 6.464A pdb=" N VAL P 73 " --> pdb=" O THR P 96 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE P 98 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA P 75 " --> pdb=" O ILE P 98 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL P 74 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL P 158 " --> pdb=" O VAL P 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 42 through 49 removed outlier: 3.969A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU Q 96 " --> pdb=" O TRP Q 29 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR Q 98 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS Q 33 " --> pdb=" O THR Q 98 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE Q 100 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN Q 99 " --> pdb=" O VAL Q 88 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL Q 88 " --> pdb=" O ASN Q 99 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS Q 101 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU Q 86 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET Q 103 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE Q 84 " --> pdb=" O MET Q 103 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE Q 105 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG Q 82 " --> pdb=" O PHE Q 105 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL Q 88 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG Q 64 " --> pdb=" O VAL Q 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 42 through 49 removed outlier: 3.969A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU Q 96 " --> pdb=" O TRP Q 29 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR Q 98 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS Q 33 " --> pdb=" O THR Q 98 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE Q 100 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 13.857A pdb=" N ASN Q 99 " --> pdb=" O LYS Q 219 " (cutoff:3.500A) removed outlier: 13.255A pdb=" N LYS Q 219 " --> pdb=" O ASN Q 99 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N HIS Q 101 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU Q 217 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE Q 105 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N ARG Q 213 " --> pdb=" O PHE Q 105 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE Q 210 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE Q 140 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL Q 212 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE Q 138 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS Q 214 " --> pdb=" O ARG Q 136 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG Q 136 " --> pdb=" O LYS Q 214 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS Q 216 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL Q 134 " --> pdb=" O LYS Q 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 77 through 86 removed outlier: 5.138A pdb=" N ASP R 78 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY R 105 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL R 80 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL R 103 " --> pdb=" O VAL R 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN R 82 " --> pdb=" O VAL R 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 141 through 142 Processing sheet with id=AB8, first strand: chain 'R' and resid 158 through 162 removed outlier: 3.625A pdb=" N THR R 198 " --> pdb=" O VAL R 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AC1, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.814A pdb=" N TYR S 138 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL S 129 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL S 140 " --> pdb=" O LYS S 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP S 163 " --> pdb=" O ILE S 169 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE S 169 " --> pdb=" O ASP S 163 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 217 through 221 removed outlier: 3.836A pdb=" N HIS S 197 " --> pdb=" O HIS S 209 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS S 211 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE S 195 " --> pdb=" O LYS S 211 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.790A pdb=" N GLY T 54 " --> pdb=" O ALA T 110 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL T 112 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE T 52 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL T 114 " --> pdb=" O PHE T 50 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE T 50 " --> pdb=" O VAL T 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 72 through 77 removed outlier: 3.645A pdb=" N LYS T 93 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 160 through 164 Processing sheet with id=AC7, first strand: chain 'U' and resid 45 through 50 removed outlier: 3.703A pdb=" N SER U 45 " --> pdb=" O PHE U 61 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS U 56 " --> pdb=" O HIS U 89 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE U 91 " --> pdb=" O LYS U 56 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU U 58 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU U 93 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE U 60 " --> pdb=" O LEU U 93 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU U 95 " --> pdb=" O ILE U 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL U 62 " --> pdb=" O GLU U 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 181 through 184 removed outlier: 3.709A pdb=" N GLY U 137 " --> pdb=" O LEU U 153 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE b 50 " --> pdb=" O TYR U 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 37 through 38 removed outlier: 6.378A pdb=" N ARG V 42 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 62 through 66 removed outlier: 7.220A pdb=" N ILE V 78 " --> pdb=" O ASP V 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP V 105 " --> pdb=" O ILE V 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY V 80 " --> pdb=" O GLN V 103 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE V 101 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N GLY V 181 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN V 64 " --> pdb=" O GLY V 181 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE V 183 " --> pdb=" O ASN V 64 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER V 66 " --> pdb=" O ILE V 183 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 139 through 140 Processing sheet with id=AD3, first strand: chain 'X' and resid 70 through 77 removed outlier: 18.342A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 15.650A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL X 85 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N PHE X 137 " --> pdb=" O ASN X 106 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL X 139 " --> pdb=" O PRO X 108 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N HIS X 110 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N LYS X 141 " --> pdb=" O HIS X 110 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR X 124 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL X 142 " --> pdb=" O ILE X 122 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE X 122 " --> pdb=" O VAL X 142 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 38 through 40 removed outlier: 6.953A pdb=" N VAL Z 30 " --> pdb=" O ILE Z 39 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL Z 79 " --> pdb=" O GLY Z 113 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE Z 115 " --> pdb=" O VAL Z 79 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL Z 81 " --> pdb=" O ILE Z 115 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP Z 117 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE Z 83 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 32 through 39 removed outlier: 6.511A pdb=" N GLU a 49 " --> pdb=" O LYS a 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 71 through 74 removed outlier: 3.714A pdb=" N GLY b 123 " --> pdb=" O VAL b 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 71 through 74 removed outlier: 6.819A pdb=" N ILE b 103 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE b 128 " --> pdb=" O TYR b 101 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR b 101 " --> pdb=" O PHE b 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 130 through 131 removed outlier: 6.614A pdb=" N LEU c 103 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL c 127 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU c 101 " --> pdb=" O VAL c 127 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL c 53 " --> pdb=" O GLN c 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN c 75 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU c 55 " --> pdb=" O ARG c 73 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE c 122 " --> pdb=" O THR c 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 6 through 15 removed outlier: 4.542A pdb=" N VAL d 12 " --> pdb=" O GLN d 22 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN d 22 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER d 14 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG d 20 " --> pdb=" O SER d 14 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS d 68 " --> pdb=" O THR d 62 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR d 62 " --> pdb=" O LYS d 68 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL d 70 " --> pdb=" O PHE d 60 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE d 60 " --> pdb=" O VAL d 70 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 44 through 47 Processing sheet with id=AE2, first strand: chain 'f' and resid 64 through 65 Processing sheet with id=AE3, first strand: chain 'o' and resid 62 through 64 removed outlier: 6.427A pdb=" N PHE o 34 " --> pdb=" O LYS o 63 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR o 35 " --> pdb=" O LEU o 12 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE o 13 " --> pdb=" O ALA o 268 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'o' and resid 310 through 311 removed outlier: 4.434A pdb=" N ALA o 336 " --> pdb=" O HIS o 349 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'p' and resid 95 through 100 removed outlier: 4.292A pdb=" N GLU p 95 " --> pdb=" O THR p 141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'p' and resid 181 through 186 Processing sheet with id=AE7, first strand: chain 'r' and resid 102 through 103 removed outlier: 3.806A pdb=" N MET r 122 " --> pdb=" O TYR r 110 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP r 181 " --> pdb=" O VAL r 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'r' and resid 195 through 196 Processing sheet with id=AE9, first strand: chain 'r' and resid 225 through 226 Processing sheet with id=AF1, first strand: chain 't' and resid 123 through 128 removed outlier: 6.621A pdb=" N ILE t 85 " --> pdb=" O PHE t 157 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL t 159 " --> pdb=" O ILE t 85 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR t 87 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY t 161 " --> pdb=" O THR t 87 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL t 89 " --> pdb=" O GLY t 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 't' and resid 336 through 338 removed outlier: 4.468A pdb=" N GLN t 302 " --> pdb=" O ARG t 562 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE t 560 " --> pdb=" O ASN t 304 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE t 306 " --> pdb=" O ARG t 558 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG t 558 " --> pdb=" O ILE t 306 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS t 308 " --> pdb=" O ARG t 556 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG t 556 " --> pdb=" O LYS t 308 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR t 281 " --> pdb=" O ALA t 261 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA t 261 " --> pdb=" O THR t 281 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 't' and resid 628 through 630 removed outlier: 7.255A pdb=" N VAL t 593 " --> pdb=" O ALA t 691 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA t 691 " --> pdb=" O VAL t 593 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN t 595 " --> pdb=" O LEU t 689 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR t 687 " --> pdb=" O SER t 597 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU t 682 " --> pdb=" O LYS t 671 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS t 671 " --> pdb=" O LEU t 682 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG t 621 " --> pdb=" O TYR t 618 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 't' and resid 639 through 641 removed outlier: 4.875A pdb=" N LEU t 697 " --> pdb=" O MET t 777 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE t 745 " --> pdb=" O THR t 758 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR t 758 " --> pdb=" O ILE t 745 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU t 747 " --> pdb=" O LYS t 756 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR t 754 " --> pdb=" O LEU t 749 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR t 716 " --> pdb=" O PHE t 708 " (cutoff:3.500A) 1685 hydrogen bonds defined for protein. 4659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1143 hydrogen bonds 1800 hydrogen bond angles 0 basepair planarities 472 basepair parallelities 811 stacking parallelities Total time for adding SS restraints: 55.28 Time building geometry restraints manager: 27.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9886 1.32 - 1.44: 28504 1.44 - 1.57: 35677 1.57 - 1.69: 3059 1.69 - 1.81: 150 Bond restraints: 77276 Sorted by residual: bond pdb=" CB ASN W 38 " pdb=" CG ASN W 38 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.33e+00 bond pdb=" C4' U 21535 " pdb=" O4' U 21535 " ideal model delta sigma weight residual 1.451 1.420 0.031 1.50e-02 4.44e+03 4.24e+00 bond pdb=" O4' U 21535 " pdb=" C1' U 21535 " ideal model delta sigma weight residual 1.412 1.382 0.030 1.50e-02 4.44e+03 3.88e+00 bond pdb=" CB VAL d 57 " pdb=" CG1 VAL d 57 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.82e+00 bond pdb=" CB THR d 62 " pdb=" CG2 THR d 62 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.71e+00 ... (remaining 77271 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.08: 9189 106.08 - 113.25: 44359 113.25 - 120.41: 29913 120.41 - 127.58: 25096 127.58 - 134.75: 3141 Bond angle restraints: 111698 Sorted by residual: angle pdb=" C3' U 21390 " pdb=" O3' U 21390 " pdb=" P A 21391 " ideal model delta sigma weight residual 120.20 128.57 -8.37 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C3' G 2 514 " pdb=" O3' G 2 514 " pdb=" P A 2 515 " ideal model delta sigma weight residual 120.20 128.49 -8.29 1.50e+00 4.44e-01 3.06e+01 angle pdb=" C2' U 21343 " pdb=" C1' U 21343 " pdb=" N1 U 21343 " ideal model delta sigma weight residual 112.00 120.14 -8.14 1.50e+00 4.44e-01 2.95e+01 angle pdb=" C4' G 2 514 " pdb=" C3' G 2 514 " pdb=" O3' G 2 514 " ideal model delta sigma weight residual 109.40 117.17 -7.77 1.50e+00 4.44e-01 2.68e+01 angle pdb=" C3' C 21332 " pdb=" O3' C 21332 " pdb=" P C 21333 " ideal model delta sigma weight residual 120.20 127.69 -7.49 1.50e+00 4.44e-01 2.49e+01 ... (remaining 111693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 44812 35.87 - 71.74: 2961 71.74 - 107.61: 357 107.61 - 143.48: 37 143.48 - 179.35: 29 Dihedral angle restraints: 48196 sinusoidal: 33845 harmonic: 14351 Sorted by residual: dihedral pdb=" C5' A 21344 " pdb=" C4' A 21344 " pdb=" C3' A 21344 " pdb=" O3' A 21344 " ideal model delta sinusoidal sigma weight residual 147.00 73.24 73.76 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C4' A 21344 " pdb=" C3' A 21344 " pdb=" C2' A 21344 " pdb=" C1' A 21344 " ideal model delta sinusoidal sigma weight residual -35.00 31.42 -66.42 1 8.00e+00 1.56e-02 9.00e+01 dihedral pdb=" C5' C 21711 " pdb=" C4' C 21711 " pdb=" C3' C 21711 " pdb=" O3' C 21711 " ideal model delta sinusoidal sigma weight residual 147.00 81.79 65.21 1 8.00e+00 1.56e-02 8.71e+01 ... (remaining 48193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 12568 0.101 - 0.203: 1030 0.203 - 0.304: 67 0.304 - 0.405: 10 0.405 - 0.507: 3 Chirality restraints: 13678 Sorted by residual: chirality pdb=" C3' G 2 514 " pdb=" C4' G 2 514 " pdb=" O3' G 2 514 " pdb=" C2' G 2 514 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" C3' C 21568 " pdb=" C4' C 21568 " pdb=" O3' C 21568 " pdb=" C2' C 21568 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C3' G 21297 " pdb=" C4' G 21297 " pdb=" O3' G 21297 " pdb=" C2' G 21297 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 13675 not shown) Planarity restraints: 8578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 21343 " 0.071 2.00e-02 2.50e+03 4.01e-02 3.62e+01 pdb=" N1 U 21343 " -0.092 2.00e-02 2.50e+03 pdb=" C2 U 21343 " 0.016 2.00e-02 2.50e+03 pdb=" O2 U 21343 " -0.015 2.00e-02 2.50e+03 pdb=" N3 U 21343 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U 21343 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U 21343 " 0.013 2.00e-02 2.50e+03 pdb=" C5 U 21343 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U 21343 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 21062 " -0.041 2.00e-02 2.50e+03 3.12e-02 2.68e+01 pdb=" N9 A 21062 " 0.085 2.00e-02 2.50e+03 pdb=" C8 A 21062 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 21062 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A 21062 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A 21062 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 21062 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A 21062 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 21062 " 0.009 2.00e-02 2.50e+03 pdb=" N3 A 21062 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A 21062 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21653 " -0.045 2.00e-02 2.50e+03 3.32e-02 2.49e+01 pdb=" N1 C 21653 " 0.082 2.00e-02 2.50e+03 pdb=" C2 C 21653 " -0.031 2.00e-02 2.50e+03 pdb=" O2 C 21653 " 0.008 2.00e-02 2.50e+03 pdb=" N3 C 21653 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 21653 " -0.009 2.00e-02 2.50e+03 pdb=" N4 C 21653 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C 21653 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C 21653 " 0.002 2.00e-02 2.50e+03 ... (remaining 8575 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 783 2.61 - 3.18: 58925 3.18 - 3.76: 117185 3.76 - 4.33: 170291 4.33 - 4.90: 244972 Nonbonded interactions: 592156 Sorted by model distance: nonbonded pdb=" O2' A 21300 " pdb=" O4' U 21301 " model vdw 2.038 2.440 nonbonded pdb=" O2' U 21390 " pdb=" OP2 A 21391 " model vdw 2.075 2.440 nonbonded pdb=" O4 U 21335 " pdb=" O6 G 21416 " model vdw 2.149 2.432 nonbonded pdb=" O2' U 2 578 " pdb=" OP1 A 2 579 " model vdw 2.154 2.440 nonbonded pdb=" O2' C 21332 " pdb=" OP2 C 21333 " model vdw 2.157 2.440 ... (remaining 592151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 15.390 Check model and map are aligned: 0.850 Set scattering table: 0.500 Process input model: 198.540 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 77276 Z= 0.530 Angle : 0.860 12.355 111698 Z= 0.488 Chirality : 0.058 0.507 13678 Planarity : 0.009 0.183 8578 Dihedral : 20.546 179.350 39052 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.48 % Favored : 96.22 % Rotamer: Outliers : 0.79 % Allowed : 3.57 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 5003 helix: -1.03 (0.11), residues: 1714 sheet: 0.31 (0.17), residues: 776 loop : -0.39 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 195 HIS 0.014 0.002 HIS W 124 PHE 0.029 0.002 PHE W 146 TYR 0.033 0.002 TYR T 84 ARG 0.035 0.003 ARG Y 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 550 time to evaluate : 4.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8761 (tm-30) REVERT: C 81 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8678 (mmmt) REVERT: C 92 ASP cc_start: 0.8369 (t0) cc_final: 0.8162 (t0) REVERT: C 97 ASN cc_start: 0.8511 (t0) cc_final: 0.8232 (t0) REVERT: E 16 SER cc_start: 0.9157 (p) cc_final: 0.8818 (t) REVERT: E 21 ASP cc_start: 0.9039 (t0) cc_final: 0.8664 (t70) REVERT: E 22 LEU cc_start: 0.9504 (tp) cc_final: 0.9250 (pt) REVERT: E 28 MET cc_start: 0.8430 (ttm) cc_final: 0.8189 (ttm) REVERT: E 31 GLU cc_start: 0.8837 (pt0) cc_final: 0.8195 (pm20) REVERT: E 32 ASP cc_start: 0.8479 (m-30) cc_final: 0.7921 (m-30) REVERT: E 64 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8819 (tttt) REVERT: E 104 GLN cc_start: 0.8887 (tt0) cc_final: 0.8025 (pm20) REVERT: F 94 GLN cc_start: 0.9377 (tm-30) cc_final: 0.9175 (tm-30) REVERT: F 98 ASP cc_start: 0.8865 (p0) cc_final: 0.8347 (p0) REVERT: H 23 ASP cc_start: 0.8695 (p0) cc_final: 0.8493 (p0) REVERT: H 60 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8061 (mt-10) REVERT: H 71 GLN cc_start: 0.8993 (tp40) cc_final: 0.8763 (tm-30) REVERT: H 91 ASP cc_start: 0.8943 (t0) cc_final: 0.8706 (t0) REVERT: I 8 ASP cc_start: 0.9036 (m-30) cc_final: 0.8820 (m-30) REVERT: I 49 ASP cc_start: 0.8912 (t0) cc_final: 0.8230 (t0) REVERT: K 44 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8105 (tp40) REVERT: K 48 ASP cc_start: 0.9037 (m-30) cc_final: 0.8482 (m-30) REVERT: K 53 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8853 (mt-10) REVERT: K 58 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8485 (mtp180) REVERT: L 58 GLU cc_start: 0.8369 (tp30) cc_final: 0.8000 (tm-30) REVERT: P 154 GLU cc_start: 0.8807 (mp0) cc_final: 0.8450 (mp0) REVERT: Q 229 MET cc_start: 0.9155 (mmm) cc_final: 0.8726 (mmm) REVERT: R 70 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8646 (t0) REVERT: S 250 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8611 (mt-10) REVERT: U 155 ASP cc_start: 0.9115 (t0) cc_final: 0.8855 (t0) REVERT: V 105 ASP cc_start: 0.8925 (t0) cc_final: 0.8522 (t0) REVERT: W 63 ASP cc_start: 0.8851 (t0) cc_final: 0.8423 (t0) REVERT: W 161 THR cc_start: 0.9604 (p) cc_final: 0.9329 (t) REVERT: X 121 ASP cc_start: 0.8914 (m-30) cc_final: 0.8692 (m-30) REVERT: Y 36 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8769 (mm-40) REVERT: Z 12 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7877 (mm-40) REVERT: a 7 GLN cc_start: 0.8177 (mt0) cc_final: 0.7962 (mt0) REVERT: a 44 ARG cc_start: 0.8393 (mtt180) cc_final: 0.7796 (mtt-85) REVERT: a 49 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8431 (mp0) REVERT: b 23 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8520 (mmt90) REVERT: b 85 ASP cc_start: 0.8799 (m-30) cc_final: 0.8595 (m-30) REVERT: d 26 ASP cc_start: 0.8925 (t0) cc_final: 0.8649 (t70) REVERT: o 24 TYR cc_start: 0.8392 (p90) cc_final: 0.7744 (p90) REVERT: o 27 TYR cc_start: 0.8070 (m-80) cc_final: 0.7847 (m-10) REVERT: o 30 TYR cc_start: 0.7900 (m-10) cc_final: 0.7676 (m-10) REVERT: p 94 PHE cc_start: 0.7776 (t80) cc_final: 0.7508 (t80) REVERT: p 95 GLU cc_start: 0.8647 (pt0) cc_final: 0.8286 (pm20) REVERT: p 131 ASN cc_start: 0.7535 (t0) cc_final: 0.6749 (p0) REVERT: p 142 ASN cc_start: 0.8708 (t0) cc_final: 0.8361 (t0) REVERT: r 152 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6604 (pmm) REVERT: r 270 GLN cc_start: 0.8749 (pt0) cc_final: 0.8484 (pp30) REVERT: t 780 MET cc_start: 0.8731 (mpp) cc_final: 0.8429 (mpt) outliers start: 33 outliers final: 10 residues processed: 581 average time/residue: 1.7253 time to fit residues: 1282.3348 Evaluate side-chains 442 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 430 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain t residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 552 optimal weight: 1.9990 chunk 495 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 334 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 512 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 593 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN B 224 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN I 23 GLN I 77 ASN K 44 GLN K 95 HIS P 23 HIS Q 101 HIS Q 157 GLN Q 183 GLN S 153 ASN S 258 GLN T 10 ASN U 29 ASN ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 161 GLN V 32 GLN V 64 ASN W 133 HIS Y 105 ASN a 75 ASN b 42 GLN c 18 HIS c 27 ASN d 110 GLN o 52 ASN o 107 ASN o 280 GLN o 305 HIS o 361 ASN o 372 ASN o 374 GLN o 406 GLN p 262 ASN r 78 ASN ** r 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 222 ASN ** r 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN t 134 ASN t 237 ASN t 294 HIS t 340 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 77276 Z= 0.165 Angle : 0.655 11.824 111698 Z= 0.347 Chirality : 0.042 0.302 13678 Planarity : 0.005 0.069 8578 Dihedral : 21.611 178.644 29305 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.30 % Favored : 97.56 % Rotamer: Outliers : 1.58 % Allowed : 8.52 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 5003 helix: 0.65 (0.12), residues: 1786 sheet: 0.35 (0.17), residues: 839 loop : -0.16 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 112 HIS 0.004 0.001 HIS p 232 PHE 0.014 0.001 PHE t 172 TYR 0.024 0.001 TYR B 209 ARG 0.007 0.000 ARG U 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 485 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8794 (tm-30) REVERT: B 145 ASP cc_start: 0.8826 (t0) cc_final: 0.8556 (t0) REVERT: C 81 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8197 (mmmt) REVERT: C 92 ASP cc_start: 0.8294 (t0) cc_final: 0.8083 (t0) REVERT: C 97 ASN cc_start: 0.8446 (t0) cc_final: 0.8166 (t0) REVERT: E 16 SER cc_start: 0.9144 (p) cc_final: 0.8817 (t) REVERT: E 21 ASP cc_start: 0.8874 (t0) cc_final: 0.8591 (t70) REVERT: E 22 LEU cc_start: 0.9536 (tp) cc_final: 0.9210 (pt) REVERT: E 31 GLU cc_start: 0.8695 (pt0) cc_final: 0.8108 (pm20) REVERT: E 32 ASP cc_start: 0.8565 (m-30) cc_final: 0.8101 (m-30) REVERT: E 104 GLN cc_start: 0.8852 (tt0) cc_final: 0.8072 (pm20) REVERT: E 118 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8684 (mm-30) REVERT: F 98 ASP cc_start: 0.8288 (p0) cc_final: 0.8073 (p0) REVERT: F 120 ASP cc_start: 0.8297 (p0) cc_final: 0.8094 (p0) REVERT: H 23 ASP cc_start: 0.8642 (p0) cc_final: 0.8366 (p0) REVERT: I 27 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8498 (mtmm) REVERT: K 44 GLN cc_start: 0.8638 (tp40) cc_final: 0.8268 (tp40) REVERT: K 58 ARG cc_start: 0.8830 (mtp85) cc_final: 0.8607 (mtp180) REVERT: L 14 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8975 (ttpp) REVERT: L 31 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8037 (tm-30) REVERT: L 58 GLU cc_start: 0.8388 (tp30) cc_final: 0.8058 (tm-30) REVERT: L 64 ARG cc_start: 0.8284 (ptt180) cc_final: 0.7975 (ppt-90) REVERT: R 54 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8899 (mp0) REVERT: R 70 ASP cc_start: 0.8906 (t70) cc_final: 0.8632 (t0) REVERT: R 97 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.8054 (mtm180) REVERT: R 246 GLU cc_start: 0.8275 (mp0) cc_final: 0.7800 (mp0) REVERT: U 155 ASP cc_start: 0.9122 (t0) cc_final: 0.8828 (t0) REVERT: V 105 ASP cc_start: 0.8441 (t0) cc_final: 0.7995 (t0) REVERT: W 161 THR cc_start: 0.9635 (p) cc_final: 0.9393 (t) REVERT: X 118 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: X 121 ASP cc_start: 0.8812 (m-30) cc_final: 0.8590 (m-30) REVERT: Y 72 MET cc_start: 0.8873 (tpp) cc_final: 0.8482 (ttp) REVERT: Z 12 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7973 (mm-40) REVERT: a 7 GLN cc_start: 0.8094 (mt0) cc_final: 0.7851 (mt0) REVERT: a 49 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8369 (mp0) REVERT: b 23 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8509 (mmt90) REVERT: c 138 GLU cc_start: 0.8594 (mp0) cc_final: 0.8320 (mp0) REVERT: d 26 ASP cc_start: 0.8794 (t0) cc_final: 0.8513 (t70) REVERT: d 81 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: o 24 TYR cc_start: 0.8491 (p90) cc_final: 0.7844 (p90) REVERT: o 289 MET cc_start: 0.8417 (tpp) cc_final: 0.7801 (mmm) REVERT: p 95 GLU cc_start: 0.8263 (pt0) cc_final: 0.7889 (pm20) REVERT: p 138 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8091 (mt-10) REVERT: r 152 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6590 (pmm) REVERT: r 232 GLU cc_start: 0.8929 (pm20) cc_final: 0.8686 (pp20) REVERT: r 270 GLN cc_start: 0.8750 (pt0) cc_final: 0.8492 (pp30) REVERT: t 780 MET cc_start: 0.8584 (mpp) cc_final: 0.8344 (mpt) outliers start: 66 outliers final: 24 residues processed: 515 average time/residue: 1.6030 time to fit residues: 1074.6401 Evaluate side-chains 451 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 423 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 330 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 494 optimal weight: 0.8980 chunk 404 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 594 optimal weight: 1.9990 chunk 642 optimal weight: 8.9990 chunk 529 optimal weight: 10.0000 chunk 590 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 477 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN P 15 GLN T 197 ASN U 29 ASN ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 GLN Z 80 HIS a 75 ASN ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 26 HIS ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 205 ASN t 302 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 77276 Z= 0.300 Angle : 0.645 10.896 111698 Z= 0.341 Chirality : 0.044 0.296 13678 Planarity : 0.005 0.072 8578 Dihedral : 21.457 179.682 29297 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.10 % Favored : 96.76 % Rotamer: Outliers : 2.08 % Allowed : 10.50 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.12), residues: 5003 helix: 1.11 (0.12), residues: 1792 sheet: 0.32 (0.17), residues: 816 loop : -0.34 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 112 HIS 0.009 0.001 HIS W 124 PHE 0.022 0.002 PHE W 146 TYR 0.020 0.002 TYR T 84 ARG 0.007 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 428 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8723 (tm-30) REVERT: B 145 ASP cc_start: 0.8842 (t0) cc_final: 0.8576 (t0) REVERT: C 81 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8448 (mtpt) REVERT: C 92 ASP cc_start: 0.8354 (t0) cc_final: 0.8128 (t0) REVERT: C 97 ASN cc_start: 0.8520 (t0) cc_final: 0.8238 (t0) REVERT: E 16 SER cc_start: 0.9155 (p) cc_final: 0.8818 (t) REVERT: E 31 GLU cc_start: 0.8749 (pt0) cc_final: 0.8241 (mp0) REVERT: E 32 ASP cc_start: 0.8707 (m-30) cc_final: 0.8362 (m-30) REVERT: E 104 GLN cc_start: 0.8836 (tt0) cc_final: 0.8039 (pm20) REVERT: E 118 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8605 (mm-30) REVERT: F 40 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8546 (mm-30) REVERT: F 98 ASP cc_start: 0.8512 (p0) cc_final: 0.7693 (p0) REVERT: H 23 ASP cc_start: 0.8681 (p0) cc_final: 0.8418 (p0) REVERT: H 64 GLU cc_start: 0.8922 (pm20) cc_final: 0.8682 (pm20) REVERT: I 25 GLN cc_start: 0.8857 (tt0) cc_final: 0.8532 (tt0) REVERT: I 27 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8620 (mtmm) REVERT: K 44 GLN cc_start: 0.8734 (tp40) cc_final: 0.8292 (tp40) REVERT: K 58 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8623 (mtp180) REVERT: K 68 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8735 (ptp-170) REVERT: L 14 LYS cc_start: 0.9250 (ttmm) cc_final: 0.9001 (ttpp) REVERT: L 31 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8158 (pp20) REVERT: L 57 MET cc_start: 0.8665 (mtm) cc_final: 0.8400 (mtp) REVERT: L 58 GLU cc_start: 0.8438 (tp30) cc_final: 0.8131 (tm-30) REVERT: L 62 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7680 (tm-30) REVERT: L 64 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7914 (ppt-90) REVERT: Q 229 MET cc_start: 0.9155 (mmm) cc_final: 0.8824 (mmm) REVERT: R 70 ASP cc_start: 0.8896 (t70) cc_final: 0.8623 (t0) REVERT: R 246 GLU cc_start: 0.8304 (mp0) cc_final: 0.7811 (mp0) REVERT: S 256 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8399 (ptp90) REVERT: T 125 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8406 (p) REVERT: U 155 ASP cc_start: 0.9127 (t0) cc_final: 0.8851 (t0) REVERT: V 105 ASP cc_start: 0.8623 (t0) cc_final: 0.8343 (t0) REVERT: W 161 THR cc_start: 0.9634 (p) cc_final: 0.9378 (t) REVERT: X 118 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: Y 72 MET cc_start: 0.8883 (tpp) cc_final: 0.8552 (ttp) REVERT: Z 12 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7670 (mm-40) REVERT: a 7 GLN cc_start: 0.8258 (mt0) cc_final: 0.7992 (mt0) REVERT: a 49 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8414 (mp0) REVERT: b 87 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: c 138 GLU cc_start: 0.8695 (mp0) cc_final: 0.8334 (mp0) REVERT: d 26 ASP cc_start: 0.8773 (t0) cc_final: 0.8466 (t70) REVERT: d 81 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: o 289 MET cc_start: 0.8509 (tpp) cc_final: 0.8084 (mmm) REVERT: p 95 GLU cc_start: 0.8283 (pt0) cc_final: 0.7818 (pm20) REVERT: r 152 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6650 (pmm) REVERT: r 162 GLU cc_start: 0.8675 (tt0) cc_final: 0.8416 (tm-30) REVERT: r 168 MET cc_start: 0.9162 (tmm) cc_final: 0.8879 (tmm) REVERT: r 178 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7250 (tm-30) REVERT: r 232 GLU cc_start: 0.8983 (pm20) cc_final: 0.8743 (pp20) REVERT: r 270 GLN cc_start: 0.8774 (pt0) cc_final: 0.8494 (pp30) REVERT: t 780 MET cc_start: 0.8609 (mpp) cc_final: 0.8311 (mpt) outliers start: 87 outliers final: 40 residues processed: 470 average time/residue: 1.6227 time to fit residues: 993.8498 Evaluate side-chains 463 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 414 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 94 LYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Z residue 16 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain b residue 87 GLU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 91 ASN Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 587 optimal weight: 20.0000 chunk 447 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 597 optimal weight: 3.9990 chunk 632 optimal weight: 20.0000 chunk 311 optimal weight: 4.9990 chunk 565 optimal weight: 0.0000 chunk 170 optimal weight: 3.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS I 101 ASN P 15 GLN P 33 GLN T 65 GLN U 29 ASN ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 142 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 77276 Z= 0.203 Angle : 0.585 10.630 111698 Z= 0.308 Chirality : 0.040 0.267 13678 Planarity : 0.004 0.068 8578 Dihedral : 21.413 179.191 29297 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.88 % Favored : 96.98 % Rotamer: Outliers : 2.44 % Allowed : 11.34 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 5003 helix: 1.42 (0.13), residues: 1783 sheet: 0.34 (0.18), residues: 811 loop : -0.40 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 112 HIS 0.005 0.001 HIS W 124 PHE 0.017 0.001 PHE B 20 TYR 0.019 0.001 TYR B 209 ARG 0.005 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 431 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8720 (tm-30) REVERT: B 66 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8355 (tp-100) REVERT: B 145 ASP cc_start: 0.8775 (t0) cc_final: 0.8509 (t0) REVERT: C 80 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7896 (ptp90) REVERT: C 92 ASP cc_start: 0.8367 (t0) cc_final: 0.8135 (t0) REVERT: C 97 ASN cc_start: 0.8509 (t0) cc_final: 0.8210 (t0) REVERT: E 16 SER cc_start: 0.9168 (p) cc_final: 0.8834 (t) REVERT: E 31 GLU cc_start: 0.8726 (pt0) cc_final: 0.8140 (mp0) REVERT: E 32 ASP cc_start: 0.8710 (m-30) cc_final: 0.8414 (m-30) REVERT: E 35 LYS cc_start: 0.9234 (mptm) cc_final: 0.8887 (mptm) REVERT: E 104 GLN cc_start: 0.8828 (tt0) cc_final: 0.8055 (pm20) REVERT: E 118 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8555 (mm-30) REVERT: F 40 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8524 (mm-30) REVERT: F 98 ASP cc_start: 0.8156 (p0) cc_final: 0.7863 (p0) REVERT: F 100 GLN cc_start: 0.8364 (mp10) cc_final: 0.7935 (mp10) REVERT: H 23 ASP cc_start: 0.8664 (p0) cc_final: 0.8377 (p0) REVERT: I 25 GLN cc_start: 0.8878 (tt0) cc_final: 0.8529 (tt0) REVERT: I 27 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8617 (mtmm) REVERT: K 44 GLN cc_start: 0.8713 (tp40) cc_final: 0.8230 (tp40) REVERT: K 58 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8629 (mtp180) REVERT: L 14 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8980 (ttpp) REVERT: L 29 ARG cc_start: 0.8889 (ttm-80) cc_final: 0.8625 (ttp-170) REVERT: L 57 MET cc_start: 0.8664 (mtm) cc_final: 0.8449 (mtp) REVERT: L 58 GLU cc_start: 0.8461 (tp30) cc_final: 0.8141 (tm-30) REVERT: L 62 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7674 (tm-30) REVERT: L 64 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7950 (ppt-90) REVERT: Q 229 MET cc_start: 0.9187 (mmm) cc_final: 0.8834 (mmm) REVERT: R 70 ASP cc_start: 0.8880 (t70) cc_final: 0.8591 (t0) REVERT: R 97 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7957 (mtm180) REVERT: R 246 GLU cc_start: 0.8313 (mp0) cc_final: 0.7825 (mp0) REVERT: S 256 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8391 (ptp90) REVERT: U 50 ASP cc_start: 0.9065 (p0) cc_final: 0.8792 (t0) REVERT: V 105 ASP cc_start: 0.8502 (t0) cc_final: 0.8291 (t0) REVERT: W 161 THR cc_start: 0.9641 (p) cc_final: 0.9387 (t) REVERT: Y 72 MET cc_start: 0.8869 (tpp) cc_final: 0.8549 (ttp) REVERT: Z 12 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7608 (mm-40) REVERT: a 7 GLN cc_start: 0.8326 (mt0) cc_final: 0.8060 (mt0) REVERT: a 42 GLU cc_start: 0.8359 (tt0) cc_final: 0.7950 (tt0) REVERT: a 49 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8359 (mp0) REVERT: c 138 GLU cc_start: 0.8706 (mp0) cc_final: 0.8336 (mp0) REVERT: d 26 ASP cc_start: 0.8795 (t0) cc_final: 0.8494 (t70) REVERT: d 81 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: o 289 MET cc_start: 0.8559 (tpp) cc_final: 0.8158 (mmm) REVERT: p 95 GLU cc_start: 0.8155 (pt0) cc_final: 0.7748 (pm20) REVERT: r 122 MET cc_start: 0.8439 (tmm) cc_final: 0.8211 (tmm) REVERT: r 152 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6611 (pmm) REVERT: r 162 GLU cc_start: 0.8661 (tt0) cc_final: 0.8402 (tm-30) REVERT: r 166 MET cc_start: 0.9179 (mmt) cc_final: 0.8946 (mmm) REVERT: r 168 MET cc_start: 0.9150 (tmm) cc_final: 0.8813 (tmm) REVERT: r 270 GLN cc_start: 0.8795 (pt0) cc_final: 0.8507 (pp30) REVERT: t 777 MET cc_start: 0.8956 (mmm) cc_final: 0.8682 (mmm) REVERT: t 780 MET cc_start: 0.8580 (mpp) cc_final: 0.8338 (mpt) outliers start: 102 outliers final: 44 residues processed: 487 average time/residue: 1.5905 time to fit residues: 1014.2982 Evaluate side-chains 461 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 412 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain Q residue 131 ASP Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain p residue 100 MET Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 714 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 526 optimal weight: 7.9990 chunk 358 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 470 optimal weight: 7.9990 chunk 260 optimal weight: 0.9980 chunk 539 optimal weight: 0.6980 chunk 436 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 567 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN P 15 GLN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 77276 Z= 0.247 Angle : 0.593 10.569 111698 Z= 0.313 Chirality : 0.041 0.275 13678 Planarity : 0.004 0.070 8578 Dihedral : 21.366 179.787 29297 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 2.35 % Allowed : 12.06 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 5003 helix: 1.52 (0.13), residues: 1786 sheet: 0.38 (0.18), residues: 796 loop : -0.49 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 112 HIS 0.007 0.001 HIS W 124 PHE 0.019 0.001 PHE W 146 TYR 0.018 0.001 TYR B 209 ARG 0.009 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 425 time to evaluate : 4.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 145 ASP cc_start: 0.8771 (t0) cc_final: 0.8495 (t0) REVERT: C 92 ASP cc_start: 0.8355 (t0) cc_final: 0.8113 (t0) REVERT: C 97 ASN cc_start: 0.8537 (t0) cc_final: 0.8241 (t0) REVERT: E 16 SER cc_start: 0.9169 (p) cc_final: 0.8817 (t) REVERT: E 31 GLU cc_start: 0.8733 (pt0) cc_final: 0.8232 (mp0) REVERT: E 32 ASP cc_start: 0.8684 (m-30) cc_final: 0.8415 (m-30) REVERT: E 104 GLN cc_start: 0.8798 (tt0) cc_final: 0.8036 (pm20) REVERT: E 118 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8539 (mm-30) REVERT: F 40 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8507 (mm-30) REVERT: F 98 ASP cc_start: 0.8451 (p0) cc_final: 0.7848 (p0) REVERT: H 23 ASP cc_start: 0.8689 (p0) cc_final: 0.8410 (p0) REVERT: I 25 GLN cc_start: 0.8923 (tt0) cc_final: 0.8585 (tt0) REVERT: I 27 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8605 (mtmm) REVERT: I 138 GLN cc_start: 0.8852 (mt0) cc_final: 0.8602 (tp-100) REVERT: K 44 GLN cc_start: 0.8784 (tp40) cc_final: 0.8341 (tp40) REVERT: K 53 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8452 (mt-10) REVERT: L 29 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8653 (ttp-170) REVERT: L 31 GLU cc_start: 0.8403 (pp20) cc_final: 0.8015 (pp20) REVERT: L 33 LEU cc_start: 0.9406 (mt) cc_final: 0.9163 (mm) REVERT: L 58 GLU cc_start: 0.8432 (tp30) cc_final: 0.8111 (tm-30) REVERT: L 62 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7712 (tm-30) REVERT: L 64 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7906 (ppt-90) REVERT: Q 229 MET cc_start: 0.9193 (mmm) cc_final: 0.8944 (mmm) REVERT: R 70 ASP cc_start: 0.8846 (t70) cc_final: 0.8596 (t0) REVERT: R 97 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7945 (mtm180) REVERT: R 246 GLU cc_start: 0.8285 (mp0) cc_final: 0.7779 (mp0) REVERT: S 256 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8392 (ptp90) REVERT: T 25 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8278 (mtm-85) REVERT: T 119 GLN cc_start: 0.8866 (tp40) cc_final: 0.8226 (mp10) REVERT: U 50 ASP cc_start: 0.9041 (p0) cc_final: 0.8786 (t0) REVERT: U 159 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8848 (p) REVERT: V 105 ASP cc_start: 0.8514 (t0) cc_final: 0.8303 (t0) REVERT: W 161 THR cc_start: 0.9641 (p) cc_final: 0.9379 (t) REVERT: Y 72 MET cc_start: 0.8879 (tpp) cc_final: 0.8489 (ttp) REVERT: Z 12 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7590 (mm-40) REVERT: a 7 GLN cc_start: 0.8346 (mt0) cc_final: 0.8098 (mt0) REVERT: a 49 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8358 (mp0) REVERT: c 138 GLU cc_start: 0.8737 (mp0) cc_final: 0.8386 (mp0) REVERT: d 26 ASP cc_start: 0.8800 (t0) cc_final: 0.8491 (t70) REVERT: d 81 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8467 (mt-10) REVERT: f 80 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.8120 (ttp80) REVERT: o 289 MET cc_start: 0.8543 (tpp) cc_final: 0.8142 (mmm) REVERT: p 95 GLU cc_start: 0.8140 (pt0) cc_final: 0.7740 (pm20) REVERT: r 152 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6596 (pmm) REVERT: r 162 GLU cc_start: 0.8669 (tt0) cc_final: 0.8421 (tm-30) REVERT: r 166 MET cc_start: 0.9211 (mmt) cc_final: 0.8953 (mmm) REVERT: r 168 MET cc_start: 0.9151 (tmm) cc_final: 0.8809 (tmm) REVERT: r 270 GLN cc_start: 0.8730 (pt0) cc_final: 0.8466 (pp30) REVERT: t 777 MET cc_start: 0.8970 (mmm) cc_final: 0.8737 (mmm) REVERT: t 780 MET cc_start: 0.8554 (mpp) cc_final: 0.8306 (mpt) outliers start: 98 outliers final: 50 residues processed: 483 average time/residue: 1.5980 time to fit residues: 1004.3343 Evaluate side-chains 465 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 409 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 94 LYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 64 ARG Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 337 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 714 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 212 optimal weight: 9.9990 chunk 569 optimal weight: 0.4980 chunk 124 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 632 optimal weight: 8.9990 chunk 525 optimal weight: 30.0000 chunk 292 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN P 15 GLN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 77276 Z= 0.275 Angle : 0.607 10.512 111698 Z= 0.319 Chirality : 0.041 0.280 13678 Planarity : 0.005 0.070 8578 Dihedral : 21.342 179.553 29297 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 2.56 % Allowed : 12.47 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 5003 helix: 1.56 (0.13), residues: 1789 sheet: 0.33 (0.18), residues: 802 loop : -0.55 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 112 HIS 0.007 0.001 HIS W 124 PHE 0.020 0.001 PHE W 146 TYR 0.019 0.001 TYR B 209 ARG 0.012 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 418 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8668 (tm-30) REVERT: B 66 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8350 (tp-100) REVERT: B 145 ASP cc_start: 0.8795 (t0) cc_final: 0.8529 (t0) REVERT: C 77 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8536 (tm-30) REVERT: C 92 ASP cc_start: 0.8382 (t0) cc_final: 0.8135 (t0) REVERT: C 97 ASN cc_start: 0.8575 (t0) cc_final: 0.8126 (t0) REVERT: E 16 SER cc_start: 0.9167 (p) cc_final: 0.8819 (t) REVERT: E 31 GLU cc_start: 0.8742 (pt0) cc_final: 0.8214 (mp0) REVERT: E 32 ASP cc_start: 0.8650 (m-30) cc_final: 0.8348 (m-30) REVERT: E 104 GLN cc_start: 0.8823 (tt0) cc_final: 0.8033 (pm20) REVERT: E 118 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8683 (mm-30) REVERT: F 40 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8538 (mm-30) REVERT: H 23 ASP cc_start: 0.8670 (p0) cc_final: 0.8429 (p0) REVERT: I 27 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8935 (mtpp) REVERT: I 138 GLN cc_start: 0.8870 (mt0) cc_final: 0.8660 (tp-100) REVERT: K 44 GLN cc_start: 0.8843 (tp40) cc_final: 0.8360 (tp40) REVERT: K 53 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8506 (mt-10) REVERT: K 58 ARG cc_start: 0.8659 (mtp85) cc_final: 0.7695 (ttp80) REVERT: K 68 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8749 (ptp-170) REVERT: L 14 LYS cc_start: 0.9273 (mtpp) cc_final: 0.8950 (ttpp) REVERT: L 29 ARG cc_start: 0.8877 (ttm-80) cc_final: 0.8671 (ttp-170) REVERT: L 31 GLU cc_start: 0.8521 (pp20) cc_final: 0.8054 (pp20) REVERT: L 33 LEU cc_start: 0.9411 (mt) cc_final: 0.9170 (mm) REVERT: L 58 GLU cc_start: 0.8432 (tp30) cc_final: 0.8131 (tm-30) REVERT: L 62 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Q 229 MET cc_start: 0.9197 (mmm) cc_final: 0.8957 (mmm) REVERT: R 70 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8601 (t0) REVERT: R 97 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7943 (mtm180) REVERT: R 246 GLU cc_start: 0.8294 (mp0) cc_final: 0.7835 (mp0) REVERT: T 119 GLN cc_start: 0.8864 (tp40) cc_final: 0.8324 (mp10) REVERT: U 50 ASP cc_start: 0.9051 (p0) cc_final: 0.8813 (t0) REVERT: U 159 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8894 (p) REVERT: U 163 ASP cc_start: 0.8597 (m-30) cc_final: 0.8057 (m-30) REVERT: V 105 ASP cc_start: 0.8545 (t0) cc_final: 0.8324 (t0) REVERT: W 161 THR cc_start: 0.9644 (p) cc_final: 0.9379 (t) REVERT: Y 72 MET cc_start: 0.8885 (tpp) cc_final: 0.8553 (ttp) REVERT: Z 12 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7605 (mm-40) REVERT: a 7 GLN cc_start: 0.8427 (mt0) cc_final: 0.8173 (mt0) REVERT: a 49 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8335 (mp0) REVERT: c 138 GLU cc_start: 0.8755 (mp0) cc_final: 0.8398 (mp0) REVERT: d 26 ASP cc_start: 0.8768 (t0) cc_final: 0.8443 (t70) REVERT: d 81 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: f 2 VAL cc_start: 0.9012 (m) cc_final: 0.8733 (p) REVERT: f 36 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8894 (mtpp) REVERT: f 80 ARG cc_start: 0.8466 (mtp-110) cc_final: 0.8154 (ttp80) REVERT: p 95 GLU cc_start: 0.8157 (pt0) cc_final: 0.7756 (pm20) REVERT: p 183 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: r 86 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8035 (mmpt) REVERT: r 152 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6608 (pmm) REVERT: r 162 GLU cc_start: 0.8677 (tt0) cc_final: 0.8427 (tm-30) REVERT: r 166 MET cc_start: 0.9225 (mmt) cc_final: 0.8951 (mmm) REVERT: r 168 MET cc_start: 0.9138 (tmm) cc_final: 0.8785 (tmm) REVERT: r 270 GLN cc_start: 0.8728 (pt0) cc_final: 0.8457 (pp30) REVERT: t 720 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9049 (ttp) REVERT: t 777 MET cc_start: 0.8959 (mmm) cc_final: 0.8741 (mmm) REVERT: t 780 MET cc_start: 0.8571 (mpp) cc_final: 0.8315 (mpt) outliers start: 107 outliers final: 58 residues processed: 482 average time/residue: 1.6013 time to fit residues: 1007.3771 Evaluate side-chains 471 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 404 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 85 LYS Chi-restraints excluded: chain K residue 94 LYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 131 ASP Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 119 GLN Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 337 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain p residue 183 GLU Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 714 VAL Chi-restraints excluded: chain t residue 720 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 610 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 360 optimal weight: 0.0060 chunk 462 optimal weight: 6.9990 chunk 358 optimal weight: 20.0000 chunk 532 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 630 optimal weight: 9.9990 chunk 394 optimal weight: 6.9990 chunk 384 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 overall best weight: 4.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 104 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 25 GLN P 15 GLN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN U 29 ASN a 75 ASN o 91 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 77276 Z= 0.269 Angle : 0.607 10.517 111698 Z= 0.318 Chirality : 0.041 0.278 13678 Planarity : 0.004 0.069 8578 Dihedral : 21.322 179.674 29296 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 2.30 % Allowed : 13.40 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.12), residues: 5003 helix: 1.57 (0.13), residues: 1795 sheet: 0.34 (0.18), residues: 802 loop : -0.59 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 112 HIS 0.010 0.001 HIS Q 232 PHE 0.020 0.001 PHE W 146 TYR 0.020 0.001 TYR e 304 ARG 0.012 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 413 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8713 (tm-30) REVERT: B 66 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8366 (tp-100) REVERT: B 145 ASP cc_start: 0.8808 (t0) cc_final: 0.8549 (t0) REVERT: C 77 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8644 (tm-30) REVERT: C 92 ASP cc_start: 0.8380 (t0) cc_final: 0.8133 (t0) REVERT: C 97 ASN cc_start: 0.8583 (t0) cc_final: 0.8137 (t0) REVERT: C 103 ASP cc_start: 0.8486 (p0) cc_final: 0.8187 (p0) REVERT: E 16 SER cc_start: 0.9172 (p) cc_final: 0.8821 (t) REVERT: E 31 GLU cc_start: 0.8712 (pt0) cc_final: 0.8220 (mp0) REVERT: E 32 ASP cc_start: 0.8629 (m-30) cc_final: 0.8338 (m-30) REVERT: E 104 GLN cc_start: 0.8840 (tt0) cc_final: 0.8046 (pm20) REVERT: E 118 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8651 (mm-30) REVERT: F 40 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8534 (mm-30) REVERT: F 98 ASP cc_start: 0.8219 (p0) cc_final: 0.7773 (p0) REVERT: H 23 ASP cc_start: 0.8671 (p0) cc_final: 0.8425 (p0) REVERT: H 60 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8057 (mt-10) REVERT: I 27 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8975 (mtpp) REVERT: K 44 GLN cc_start: 0.8840 (tp40) cc_final: 0.8363 (tp40) REVERT: K 53 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8506 (mt-10) REVERT: K 58 ARG cc_start: 0.8669 (mtp85) cc_final: 0.7751 (ttp80) REVERT: K 68 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8703 (ptp-170) REVERT: L 14 LYS cc_start: 0.9282 (mtpp) cc_final: 0.8962 (ttpp) REVERT: L 31 GLU cc_start: 0.8553 (pp20) cc_final: 0.8096 (pp20) REVERT: L 33 LEU cc_start: 0.9407 (mt) cc_final: 0.9168 (mm) REVERT: L 58 GLU cc_start: 0.8410 (tp30) cc_final: 0.8176 (tm-30) REVERT: L 62 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7719 (tm-30) REVERT: Q 229 MET cc_start: 0.9215 (mmm) cc_final: 0.8960 (mpp) REVERT: R 70 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8574 (t0) REVERT: R 97 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7986 (mtm180) REVERT: R 246 GLU cc_start: 0.8295 (mp0) cc_final: 0.7768 (mp0) REVERT: S 256 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8164 (ptp90) REVERT: T 119 GLN cc_start: 0.8832 (tp40) cc_final: 0.8344 (mp10) REVERT: U 50 ASP cc_start: 0.9063 (p0) cc_final: 0.8844 (t0) REVERT: U 158 ASP cc_start: 0.9074 (p0) cc_final: 0.8822 (p0) REVERT: U 159 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8848 (p) REVERT: U 163 ASP cc_start: 0.8612 (m-30) cc_final: 0.8124 (m-30) REVERT: V 105 ASP cc_start: 0.8489 (t0) cc_final: 0.8255 (t0) REVERT: W 161 THR cc_start: 0.9660 (p) cc_final: 0.9387 (t) REVERT: Y 72 MET cc_start: 0.8860 (tpp) cc_final: 0.8481 (ttp) REVERT: Z 12 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7610 (mm-40) REVERT: a 7 GLN cc_start: 0.8434 (mt0) cc_final: 0.8195 (mt0) REVERT: a 49 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8324 (mp0) REVERT: c 138 GLU cc_start: 0.8760 (mp0) cc_final: 0.8398 (mp0) REVERT: d 26 ASP cc_start: 0.8774 (t0) cc_final: 0.8444 (t70) REVERT: d 81 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: f 2 VAL cc_start: 0.9028 (m) cc_final: 0.8773 (p) REVERT: o 289 MET cc_start: 0.8462 (mmm) cc_final: 0.8178 (mmm) REVERT: p 94 PHE cc_start: 0.7892 (t80) cc_final: 0.7684 (t80) REVERT: p 95 GLU cc_start: 0.8186 (pt0) cc_final: 0.7777 (pm20) REVERT: r 86 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8040 (mmpt) REVERT: r 152 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6627 (pmm) REVERT: r 162 GLU cc_start: 0.8674 (tt0) cc_final: 0.8431 (tm-30) REVERT: r 166 MET cc_start: 0.9228 (mmt) cc_final: 0.8953 (mmm) REVERT: r 168 MET cc_start: 0.9129 (tmm) cc_final: 0.8779 (tmm) REVERT: r 270 GLN cc_start: 0.8738 (pt0) cc_final: 0.8471 (pp30) REVERT: t 720 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9057 (ttp) REVERT: t 780 MET cc_start: 0.8563 (mpp) cc_final: 0.8313 (mpt) outliers start: 96 outliers final: 55 residues processed: 474 average time/residue: 1.6156 time to fit residues: 1002.0082 Evaluate side-chains 464 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 400 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 94 LYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 337 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 714 VAL Chi-restraints excluded: chain t residue 720 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 389 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 376 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 400 optimal weight: 5.9990 chunk 429 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 495 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 25 GLN P 15 GLN U 29 ASN a 75 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 77276 Z= 0.271 Angle : 0.608 10.608 111698 Z= 0.319 Chirality : 0.041 0.291 13678 Planarity : 0.004 0.068 8578 Dihedral : 21.303 179.860 29295 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 2.27 % Allowed : 13.85 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 5003 helix: 1.62 (0.13), residues: 1795 sheet: 0.35 (0.18), residues: 795 loop : -0.62 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 112 HIS 0.007 0.001 HIS W 124 PHE 0.025 0.001 PHE B 20 TYR 0.019 0.001 TYR B 209 ARG 0.012 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 412 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8744 (tm-30) REVERT: B 66 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8369 (tp-100) REVERT: B 145 ASP cc_start: 0.8796 (t0) cc_final: 0.8529 (t0) REVERT: C 72 LYS cc_start: 0.8618 (tmmt) cc_final: 0.8397 (tppt) REVERT: C 77 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 92 ASP cc_start: 0.8385 (t0) cc_final: 0.8135 (t0) REVERT: C 97 ASN cc_start: 0.8599 (t0) cc_final: 0.8184 (t0) REVERT: C 103 ASP cc_start: 0.8493 (p0) cc_final: 0.8208 (p0) REVERT: E 16 SER cc_start: 0.9172 (p) cc_final: 0.8821 (t) REVERT: E 31 GLU cc_start: 0.8729 (pt0) cc_final: 0.8250 (mp0) REVERT: E 32 ASP cc_start: 0.8608 (m-30) cc_final: 0.8327 (m-30) REVERT: E 104 GLN cc_start: 0.8851 (tt0) cc_final: 0.8092 (pm20) REVERT: E 118 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8667 (mm-30) REVERT: F 40 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8552 (mm-30) REVERT: H 23 ASP cc_start: 0.8669 (p0) cc_final: 0.8422 (p0) REVERT: H 60 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8077 (mt-10) REVERT: I 27 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9011 (mtpp) REVERT: K 44 GLN cc_start: 0.8862 (tp40) cc_final: 0.8446 (tp40) REVERT: K 53 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8518 (mt-10) REVERT: K 58 ARG cc_start: 0.8684 (mtp85) cc_final: 0.7774 (ttp80) REVERT: K 68 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8691 (ptp-170) REVERT: L 31 GLU cc_start: 0.8552 (pp20) cc_final: 0.8160 (pp20) REVERT: L 33 LEU cc_start: 0.9412 (mt) cc_final: 0.9121 (mm) REVERT: L 58 GLU cc_start: 0.8403 (tp30) cc_final: 0.8167 (tm-30) REVERT: L 62 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7726 (tm-30) REVERT: Q 229 MET cc_start: 0.9202 (mmm) cc_final: 0.8937 (mmm) REVERT: R 70 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8582 (t0) REVERT: R 97 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7989 (mtm180) REVERT: R 246 GLU cc_start: 0.8291 (mp0) cc_final: 0.7771 (mp0) REVERT: S 256 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8232 (ptp90) REVERT: T 119 GLN cc_start: 0.8824 (tp40) cc_final: 0.8378 (mp10) REVERT: U 50 ASP cc_start: 0.9055 (p0) cc_final: 0.8845 (t0) REVERT: U 158 ASP cc_start: 0.9046 (p0) cc_final: 0.8799 (p0) REVERT: U 159 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8842 (p) REVERT: U 163 ASP cc_start: 0.8616 (m-30) cc_final: 0.8098 (m-30) REVERT: V 105 ASP cc_start: 0.8508 (t0) cc_final: 0.8300 (t0) REVERT: W 161 THR cc_start: 0.9651 (p) cc_final: 0.9386 (t) REVERT: Y 72 MET cc_start: 0.8861 (tpp) cc_final: 0.8483 (ttp) REVERT: Z 12 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7587 (mm-40) REVERT: a 7 GLN cc_start: 0.8445 (mt0) cc_final: 0.8160 (mt0) REVERT: a 49 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8328 (mp0) REVERT: a 80 LYS cc_start: 0.9223 (tppt) cc_final: 0.8943 (mttm) REVERT: c 138 GLU cc_start: 0.8756 (mp0) cc_final: 0.8382 (mp0) REVERT: d 26 ASP cc_start: 0.8793 (t0) cc_final: 0.8456 (t70) REVERT: d 81 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: f 80 ARG cc_start: 0.8463 (mtp-110) cc_final: 0.8008 (ttp-110) REVERT: o 288 PHE cc_start: 0.8984 (p90) cc_final: 0.8728 (p90) REVERT: o 289 MET cc_start: 0.8507 (mmm) cc_final: 0.8215 (mmm) REVERT: p 94 PHE cc_start: 0.7896 (t80) cc_final: 0.7675 (t80) REVERT: p 95 GLU cc_start: 0.8181 (pt0) cc_final: 0.7821 (pm20) REVERT: r 86 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8038 (mmpt) REVERT: r 152 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6642 (pmm) REVERT: r 162 GLU cc_start: 0.8676 (tt0) cc_final: 0.8433 (tm-30) REVERT: r 166 MET cc_start: 0.9230 (mmt) cc_final: 0.8955 (mmm) REVERT: r 168 MET cc_start: 0.9115 (tmm) cc_final: 0.8768 (tmm) REVERT: r 270 GLN cc_start: 0.8740 (pt0) cc_final: 0.8470 (pp30) REVERT: t 720 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9073 (ttp) REVERT: t 780 MET cc_start: 0.8565 (mpp) cc_final: 0.8315 (mpt) outliers start: 95 outliers final: 51 residues processed: 469 average time/residue: 1.5970 time to fit residues: 982.1986 Evaluate side-chains 462 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 402 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 94 LYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 337 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 714 VAL Chi-restraints excluded: chain t residue 720 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 573 optimal weight: 0.7980 chunk 603 optimal weight: 10.0000 chunk 550 optimal weight: 6.9990 chunk 587 optimal weight: 10.0000 chunk 353 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 530 optimal weight: 0.5980 chunk 555 optimal weight: 0.7980 chunk 585 optimal weight: 6.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 25 GLN P 15 GLN U 29 ASN a 75 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 77276 Z= 0.187 Angle : 0.581 11.695 111698 Z= 0.305 Chirality : 0.039 0.263 13678 Planarity : 0.004 0.065 8578 Dihedral : 21.306 179.882 29295 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 1.68 % Allowed : 14.74 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.12), residues: 5003 helix: 1.76 (0.13), residues: 1787 sheet: 0.42 (0.18), residues: 801 loop : -0.55 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 112 HIS 0.004 0.001 HIS Z 29 PHE 0.013 0.001 PHE W 146 TYR 0.017 0.001 TYR K 57 ARG 0.013 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 412 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8741 (tm-30) REVERT: B 66 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8339 (tp-100) REVERT: B 145 ASP cc_start: 0.8801 (t0) cc_final: 0.8534 (t0) REVERT: C 72 LYS cc_start: 0.8645 (tmmt) cc_final: 0.8437 (tppt) REVERT: C 80 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7975 (ptp90) REVERT: C 92 ASP cc_start: 0.8370 (t0) cc_final: 0.8123 (t0) REVERT: C 97 ASN cc_start: 0.8582 (t0) cc_final: 0.8164 (t0) REVERT: C 103 ASP cc_start: 0.8469 (p0) cc_final: 0.8180 (p0) REVERT: E 16 SER cc_start: 0.9201 (p) cc_final: 0.8860 (t) REVERT: E 31 GLU cc_start: 0.8714 (pt0) cc_final: 0.8251 (mp0) REVERT: E 32 ASP cc_start: 0.8602 (m-30) cc_final: 0.8316 (m-30) REVERT: E 104 GLN cc_start: 0.8861 (tt0) cc_final: 0.8116 (pm20) REVERT: E 118 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8474 (mm-30) REVERT: F 40 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8539 (mm-30) REVERT: F 63 ILE cc_start: 0.9746 (pt) cc_final: 0.9475 (pp) REVERT: H 23 ASP cc_start: 0.8644 (p0) cc_final: 0.8378 (p0) REVERT: H 60 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8063 (mt-10) REVERT: H 63 GLN cc_start: 0.8129 (pm20) cc_final: 0.7876 (tm-30) REVERT: H 64 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8538 (tm-30) REVERT: I 27 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9007 (mtpp) REVERT: I 138 GLN cc_start: 0.8951 (tt0) cc_final: 0.8631 (tp-100) REVERT: K 44 GLN cc_start: 0.8850 (tp40) cc_final: 0.8416 (tp40) REVERT: K 53 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8515 (mt-10) REVERT: K 58 ARG cc_start: 0.8696 (mtp85) cc_final: 0.7810 (ttp80) REVERT: L 31 GLU cc_start: 0.8554 (pp20) cc_final: 0.8145 (pp20) REVERT: L 33 LEU cc_start: 0.9352 (mt) cc_final: 0.9127 (mm) REVERT: L 58 GLU cc_start: 0.8403 (tp30) cc_final: 0.8193 (tm-30) REVERT: L 62 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7754 (tm-30) REVERT: P 110 TYR cc_start: 0.8670 (p90) cc_final: 0.8436 (p90) REVERT: Q 229 MET cc_start: 0.9218 (mmm) cc_final: 0.8965 (mmm) REVERT: R 70 ASP cc_start: 0.8842 (t70) cc_final: 0.8574 (t0) REVERT: R 246 GLU cc_start: 0.8269 (mp0) cc_final: 0.7725 (mp0) REVERT: S 256 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8258 (ptp90) REVERT: T 119 GLN cc_start: 0.8766 (tp40) cc_final: 0.8334 (mp10) REVERT: U 158 ASP cc_start: 0.9019 (p0) cc_final: 0.8762 (p0) REVERT: U 159 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8806 (p) REVERT: U 163 ASP cc_start: 0.8603 (m-30) cc_final: 0.8067 (m-30) REVERT: W 161 THR cc_start: 0.9651 (p) cc_final: 0.9389 (t) REVERT: Y 72 MET cc_start: 0.8867 (tpp) cc_final: 0.8505 (ttp) REVERT: a 7 GLN cc_start: 0.8411 (mt0) cc_final: 0.8131 (mt0) REVERT: a 49 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8552 (mp0) REVERT: a 80 LYS cc_start: 0.9222 (tppt) cc_final: 0.8948 (mttm) REVERT: c 138 GLU cc_start: 0.8744 (mp0) cc_final: 0.8369 (mp0) REVERT: d 26 ASP cc_start: 0.8766 (t0) cc_final: 0.8438 (t70) REVERT: f 80 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8148 (ttp80) REVERT: o 289 MET cc_start: 0.8480 (mmm) cc_final: 0.8216 (mmm) REVERT: p 95 GLU cc_start: 0.8129 (pt0) cc_final: 0.7778 (pm20) REVERT: r 86 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8022 (mmpt) REVERT: r 152 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6654 (pmm) REVERT: r 162 GLU cc_start: 0.8666 (tt0) cc_final: 0.8414 (tm-30) REVERT: r 166 MET cc_start: 0.9229 (mmt) cc_final: 0.8955 (mmm) REVERT: r 168 MET cc_start: 0.9104 (tmm) cc_final: 0.8767 (tmm) REVERT: r 270 GLN cc_start: 0.8734 (pt0) cc_final: 0.8461 (pp30) REVERT: t 720 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9055 (ttp) REVERT: t 777 MET cc_start: 0.8920 (mmm) cc_final: 0.8564 (mmm) REVERT: t 780 MET cc_start: 0.8548 (mpp) cc_final: 0.8303 (mpt) outliers start: 70 outliers final: 45 residues processed: 455 average time/residue: 1.6569 time to fit residues: 984.9862 Evaluate side-chains 454 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 403 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 337 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 88 ILE Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 720 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 385 optimal weight: 3.9990 chunk 621 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 chunk 431 optimal weight: 4.9990 chunk 651 optimal weight: 6.9990 chunk 599 optimal weight: 10.0000 chunk 518 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 400 optimal weight: 0.0050 chunk 318 optimal weight: 4.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 25 GLN K 38 HIS P 15 GLN U 29 ASN a 75 ASN ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 77276 Z= 0.211 Angle : 0.582 12.244 111698 Z= 0.305 Chirality : 0.039 0.269 13678 Planarity : 0.004 0.065 8578 Dihedral : 21.265 179.996 29295 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.56 % Favored : 96.30 % Rotamer: Outliers : 1.56 % Allowed : 14.88 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 5003 helix: 1.78 (0.13), residues: 1787 sheet: 0.37 (0.18), residues: 807 loop : -0.55 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 112 HIS 0.005 0.001 HIS W 124 PHE 0.026 0.001 PHE B 20 TYR 0.013 0.001 TYR r 210 ARG 0.015 0.000 ARG U 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 409 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8741 (tm-30) REVERT: B 66 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8379 (tp-100) REVERT: B 145 ASP cc_start: 0.8800 (t0) cc_final: 0.8528 (t0) REVERT: C 92 ASP cc_start: 0.8373 (t0) cc_final: 0.8127 (t0) REVERT: C 97 ASN cc_start: 0.8596 (t0) cc_final: 0.8182 (t0) REVERT: C 103 ASP cc_start: 0.8463 (p0) cc_final: 0.8168 (p0) REVERT: E 16 SER cc_start: 0.9208 (p) cc_final: 0.8867 (t) REVERT: E 31 GLU cc_start: 0.8745 (pt0) cc_final: 0.8236 (mp0) REVERT: E 32 ASP cc_start: 0.8568 (m-30) cc_final: 0.8285 (m-30) REVERT: E 104 GLN cc_start: 0.8881 (tt0) cc_final: 0.8071 (pm20) REVERT: E 118 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8438 (mm-30) REVERT: F 40 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8550 (mm-30) REVERT: F 63 ILE cc_start: 0.9758 (pt) cc_final: 0.9487 (pp) REVERT: H 23 ASP cc_start: 0.8633 (p0) cc_final: 0.8391 (p0) REVERT: H 60 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8051 (mt-10) REVERT: H 63 GLN cc_start: 0.8159 (pm20) cc_final: 0.7844 (tm-30) REVERT: H 64 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8629 (tm-30) REVERT: I 27 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9015 (mtpp) REVERT: I 138 GLN cc_start: 0.8958 (tt0) cc_final: 0.8642 (tp-100) REVERT: K 44 GLN cc_start: 0.8820 (tp40) cc_final: 0.8365 (tp40) REVERT: K 53 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8529 (mt-10) REVERT: K 58 ARG cc_start: 0.8708 (mtp85) cc_final: 0.7950 (ttt-90) REVERT: L 14 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8864 (ttpp) REVERT: L 31 GLU cc_start: 0.8580 (pp20) cc_final: 0.8173 (pp20) REVERT: L 33 LEU cc_start: 0.9369 (mt) cc_final: 0.9165 (mm) REVERT: L 58 GLU cc_start: 0.8410 (tp30) cc_final: 0.8192 (tm-30) REVERT: L 62 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7744 (tm-30) REVERT: Q 229 MET cc_start: 0.9216 (mmm) cc_final: 0.8984 (mmm) REVERT: R 70 ASP cc_start: 0.8839 (t70) cc_final: 0.8569 (t0) REVERT: R 246 GLU cc_start: 0.8280 (mp0) cc_final: 0.7744 (mp0) REVERT: S 256 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8255 (ptp90) REVERT: T 119 GLN cc_start: 0.8748 (tp40) cc_final: 0.8325 (mp10) REVERT: U 158 ASP cc_start: 0.9026 (p0) cc_final: 0.8770 (p0) REVERT: U 159 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8802 (p) REVERT: U 163 ASP cc_start: 0.8643 (m-30) cc_final: 0.8131 (m-30) REVERT: W 161 THR cc_start: 0.9655 (p) cc_final: 0.9397 (t) REVERT: Y 72 MET cc_start: 0.8873 (tpp) cc_final: 0.8501 (ttp) REVERT: Z 12 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7501 (mm-40) REVERT: a 7 GLN cc_start: 0.8389 (mt0) cc_final: 0.8119 (mt0) REVERT: a 49 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8557 (mp0) REVERT: a 80 LYS cc_start: 0.9224 (tppt) cc_final: 0.8959 (mttm) REVERT: c 138 GLU cc_start: 0.8747 (mp0) cc_final: 0.8378 (mp0) REVERT: d 26 ASP cc_start: 0.8764 (t0) cc_final: 0.8436 (t70) REVERT: f 80 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8163 (ttp80) REVERT: o 289 MET cc_start: 0.8510 (mmm) cc_final: 0.8235 (mmm) REVERT: p 94 PHE cc_start: 0.7898 (t80) cc_final: 0.7605 (t80) REVERT: p 95 GLU cc_start: 0.8095 (pt0) cc_final: 0.7769 (pm20) REVERT: r 86 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8030 (mmpt) REVERT: r 152 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6702 (pmm) REVERT: r 162 GLU cc_start: 0.8664 (tt0) cc_final: 0.8422 (tm-30) REVERT: r 166 MET cc_start: 0.9234 (mmt) cc_final: 0.8945 (mmm) REVERT: r 168 MET cc_start: 0.9093 (tmm) cc_final: 0.8744 (tmm) REVERT: r 270 GLN cc_start: 0.8741 (pt0) cc_final: 0.8466 (pp30) REVERT: t 720 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9057 (ttp) REVERT: t 777 MET cc_start: 0.8939 (mmm) cc_final: 0.8638 (mmm) REVERT: t 780 MET cc_start: 0.8524 (mpp) cc_final: 0.8288 (mpt) outliers start: 65 outliers final: 49 residues processed: 453 average time/residue: 1.6139 time to fit residues: 956.0572 Evaluate side-chains 459 residues out of total 4411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 404 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 119 GLN Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain a residue 65 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain o residue 337 VAL Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 171 SER Chi-restraints excluded: chain r residue 86 LYS Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 171 SER Chi-restraints excluded: chain r residue 247 CYS Chi-restraints excluded: chain t residue 88 ILE Chi-restraints excluded: chain t residue 191 VAL Chi-restraints excluded: chain t residue 714 VAL Chi-restraints excluded: chain t residue 720 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 412 optimal weight: 2.9990 chunk 552 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 519 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 533 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 25 GLN P 15 GLN U 29 ASN a 75 ASN b 120 HIS ** o 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.039034 restraints weight = 256377.302| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.66 r_work: 0.2590 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 77276 Z= 0.355 Angle : 0.648 12.186 111698 Z= 0.338 Chirality : 0.043 0.293 13678 Planarity : 0.005 0.071 8578 Dihedral : 21.260 179.934 29295 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 1.77 % Allowed : 15.03 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.12), residues: 5003 helix: 1.68 (0.13), residues: 1785 sheet: 0.32 (0.18), residues: 799 loop : -0.64 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 67 HIS 0.008 0.001 HIS W 124 PHE 0.025 0.002 PHE W 146 TYR 0.017 0.002 TYR P 36 ARG 0.014 0.001 ARG F 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18650.81 seconds wall clock time: 326 minutes 57.36 seconds (19617.36 seconds total)