Starting phenix.real_space_refine on Mon Sep 30 02:29:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/09_2024/8eup_24410.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/09_2024/8eup_24410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/09_2024/8eup_24410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/09_2024/8eup_24410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/09_2024/8eup_24410.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/09_2024/8eup_24410.cif" } resolution = 3.1 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= 0.008 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 1623 5.49 5 S 99 5.16 5 C 43129 2.51 5 N 14617 2.21 5 O 19253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78722 Number of models: 1 Model: "" Number of chains: 41 Chain: "1" Number of atoms: 30438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 30438 Classifications: {'RNA': 1422} Modifications used: {'rna2p_pur': 148, 'rna2p_pyr': 95, 'rna3p_pur': 650, 'rna3p_pyr': 529} Link IDs: {'rna2p': 242, 'rna3p': 1179} Chain breaks: 25 Chain: "2" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3109 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 10, 'rna3p_pur': 61, 'rna3p_pyr': 59} Link IDs: {'rna2p': 25, 'rna3p': 120} Chain breaks: 3 Chain: "3" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1613 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "4" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1746 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain: "5" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2669 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 323} Chain breaks: 1 Chain: "6" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1167 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 19, 'rna3p': 35} Chain breaks: 2 Chain: "A" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2049 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1552 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 302} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1014 Unresolved non-hydrogen angles: 1280 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 13, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 526 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2568 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3055 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 16, 'TRANS': 383} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1328 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 156} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1939 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain: "G" Number of atoms: 1277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1261 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1261 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 bond proxies already assigned to first conformer: 1261 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 862 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 281 Chain: "J" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 469 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 182 Chain: "K" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1225 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 220} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 232} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 753 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 351 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "M" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 609 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 209 Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain breaks: 1 Chain: "P" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1037 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 2 Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "V" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 619 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 149 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 749 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 282 Chain: "e" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 993 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "i" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "m" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain breaks: 1 Chain: "o" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 673 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 6, 'TRANS': 129} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 253 Chain: "r" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 278 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 140 Chain: "t" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 506 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 331 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 211 Chain: "v" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1276 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain breaks: 1 Chain: "x" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2524 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 294} Chain: "y" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 607 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 328 Chain: "T" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 125 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "j" 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 70968 SG CYS j 19 89.105 92.703 164.308 1.00 57.49 S ATOM 70996 SG CYS j 22 90.908 93.585 161.483 1.00 37.55 S ATOM 71092 SG CYS j 34 90.107 90.050 161.484 1.00 41.22 S ATOM 71109 SG CYS j 37 92.818 91.522 163.890 1.00 41.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP G 227 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.80 Time building chain proxies: 33.20, per 1000 atoms: 0.42 Number of scatterers: 78722 At special positions: 0 Unit cell: (226.84, 196.1, 311.64, 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 99 16.00 P 1623 15.00 O 19253 8.00 N 14617 7.00 C 43129 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.77 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " Number of angles added : 6 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 57 sheets defined 42.0% alpha, 15.4% beta 487 base pairs and 883 stacking pairs defined. Time for finding SS restraints: 27.82 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 128 Processing helix chain '3' and resid 137 through 156 removed outlier: 3.525A pdb=" N HIS 3 142 " --> pdb=" O PRO 3 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 172 Processing helix chain '3' and resid 182 through 194 removed outlier: 4.251A pdb=" N LYS 3 188 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 12 removed outlier: 3.919A pdb=" N ALA 4 12 " --> pdb=" O ILE 4 8 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 12' Processing helix chain '4' and resid 15 through 30 removed outlier: 4.138A pdb=" N LYS 4 21 " --> pdb=" O LYS 4 17 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 4 23 " --> pdb=" O ARG 4 19 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU 4 24 " --> pdb=" O ASP 4 20 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG 4 28 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE 4 29 " --> pdb=" O SER 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 54 removed outlier: 3.505A pdb=" N PHE 4 41 " --> pdb=" O GLU 4 37 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET 4 54 " --> pdb=" O TYR 4 50 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 70 removed outlier: 3.890A pdb=" N SER 4 65 " --> pdb=" O GLN 4 61 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP 4 66 " --> pdb=" O GLN 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 93 Processing helix chain '4' and resid 99 through 101 No H-bonds generated for 'chain '4' and resid 99 through 101' Processing helix chain '4' and resid 102 through 128 removed outlier: 4.062A pdb=" N PHE 4 106 " --> pdb=" O ARG 4 102 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE 4 118 " --> pdb=" O CYS 4 114 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS 4 126 " --> pdb=" O GLN 4 122 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 4 127 " --> pdb=" O THR 4 123 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 143 Processing helix chain '4' and resid 154 through 173 removed outlier: 3.974A pdb=" N LEU 4 158 " --> pdb=" O PRO 4 154 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR 4 166 " --> pdb=" O ALA 4 162 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU 4 167 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS 4 171 " --> pdb=" O GLU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 188 Processing helix chain '4' and resid 195 through 202 Processing helix chain '5' and resid 40 through 43 Processing helix chain '5' and resid 166 through 170 Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.328A pdb=" N ASP A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 254 through 283 removed outlier: 3.894A pdb=" N ILE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.094A pdb=" N ASN A 292 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.724A pdb=" N THR B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 removed outlier: 4.061A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.535A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.502A pdb=" N PHE C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.503A pdb=" N GLU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 4.079A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.671A pdb=" N ARG C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.395A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 97 through 107 removed outlier: 3.628A pdb=" N GLU D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.974A pdb=" N ARG D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Proline residue: D 121 - end of helix Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.578A pdb=" N ALA D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.781A pdb=" N GLY D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.597A pdb=" N LYS D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 removed outlier: 3.512A pdb=" N ILE D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 removed outlier: 4.309A pdb=" N PHE D 324 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 446 through 456 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 472 through 483 removed outlier: 4.110A pdb=" N LYS D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 503 Processing helix chain 'D' and resid 516 through 525 removed outlier: 3.571A pdb=" N GLY D 525 " --> pdb=" O ALA D 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.241A pdb=" N GLU E 142 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix removed outlier: 3.568A pdb=" N LYS E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 16 through 80 removed outlier: 3.524A pdb=" N LEU F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.889A pdb=" N LYS F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.519A pdb=" N ILE F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.413A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 241 through 247 removed outlier: 3.604A pdb=" N LEU F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 removed outlier: 3.629A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.708A pdb=" N SER G 213 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.530A pdb=" N GLY H 117 " --> pdb=" O ASN H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 134 through 160 Processing helix chain 'J' and resid 177 through 187 Processing helix chain 'K' and resid 14 through 27 Processing helix chain 'K' and resid 42 through 46 removed outlier: 3.753A pdb=" N GLU K 46 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 106 removed outlier: 3.734A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.575A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.677A pdb=" N PHE K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 155 through 160 Processing helix chain 'K' and resid 174 through 187 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'K' and resid 256 through 262 removed outlier: 3.533A pdb=" N ALA K 262 " --> pdb=" O LYS K 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.515A pdb=" N LYS L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.948A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.690A pdb=" N ASN L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS L 122 " --> pdb=" O VAL L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.503A pdb=" N MET N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 removed outlier: 3.615A pdb=" N ASN N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.531A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 58 Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 93 through 102 removed outlier: 3.883A pdb=" N GLU O 101 " --> pdb=" O GLN O 97 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.346A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 125 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 150 through 186 Processing helix chain 'O' and resid 192 through 196 removed outlier: 3.502A pdb=" N PHE O 195 " --> pdb=" O LEU O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 85 through 106 Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.531A pdb=" N LYS P 111 " --> pdb=" O ASP P 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 39 removed outlier: 3.717A pdb=" N LYS Q 30 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 51 removed outlier: 3.828A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 71 Processing helix chain 'Q' and resid 108 through 118 removed outlier: 3.672A pdb=" N ALA Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 130 Processing helix chain 'S' and resid 32 through 48 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 142 Processing helix chain 'V' and resid 121 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 5.005A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'b' and resid 15 through 30 Processing helix chain 'b' and resid 41 through 68 Processing helix chain 'b' and resid 94 through 120 Processing helix chain 'b' and resid 122 through 160 removed outlier: 3.666A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 440 through 445 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.682A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU e 80 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU e 81 " --> pdb=" O SER e 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 75 through 81' Processing helix chain 'e' and resid 82 through 84 No H-bonds generated for 'chain 'e' and resid 82 through 84' Processing helix chain 'e' and resid 98 through 113 removed outlier: 3.576A pdb=" N GLU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 43 removed outlier: 3.540A pdb=" N GLN f 43 " --> pdb=" O LYS f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 46 No H-bonds generated for 'chain 'f' and resid 44 through 46' Processing helix chain 'f' and resid 91 through 95 removed outlier: 4.041A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 Processing helix chain 'h' and resid 12 through 36 removed outlier: 4.234A pdb=" N LEU h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU h 23 " --> pdb=" O GLN h 19 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.013A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 92 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.659A pdb=" N PHE i 37 " --> pdb=" O LYS i 33 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY i 47 " --> pdb=" O ARG i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 62 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 99 Processing helix chain 'j' and resid 50 through 57 Processing helix chain 'j' and resid 66 through 74 removed outlier: 3.957A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 249 through 256 Processing helix chain 'o' and resid 117 through 129 removed outlier: 3.614A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 167 Processing helix chain 'o' and resid 187 through 192 Processing helix chain 'o' and resid 202 through 213 Processing helix chain 'o' and resid 216 through 225 Processing helix chain 'o' and resid 226 through 238 Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.184A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 57 removed outlier: 3.577A pdb=" N LYS r 48 " --> pdb=" O GLY r 44 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 72 removed outlier: 3.985A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.633A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 58 removed outlier: 3.506A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.589A pdb=" N LEU u 113 " --> pdb=" O TYR u 109 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 12 removed outlier: 3.988A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 Processing helix chain 'v' and resid 45 through 53 Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 194 through 207 removed outlier: 3.687A pdb=" N LYS v 206 " --> pdb=" O TYR v 202 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA v 207 " --> pdb=" O ILE v 203 " (cutoff:3.500A) Processing helix chain 'x' and resid 6 through 39 Processing helix chain 'x' and resid 39 through 50 removed outlier: 3.757A pdb=" N LYS x 43 " --> pdb=" O ASP x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 79 removed outlier: 3.524A pdb=" N GLN x 75 " --> pdb=" O ASP x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 88 Processing helix chain 'x' and resid 105 through 110 removed outlier: 4.044A pdb=" N TYR x 109 " --> pdb=" O SER x 105 " (cutoff:3.500A) Processing helix chain 'x' and resid 111 through 119 Processing helix chain 'x' and resid 132 through 144 removed outlier: 3.848A pdb=" N GLU x 138 " --> pdb=" O HIS x 134 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS x 142 " --> pdb=" O GLU x 138 " (cutoff:3.500A) Processing helix chain 'x' and resid 205 through 218 Processing helix chain 'x' and resid 296 through 300 Processing helix chain 'y' and resid 12 through 17 Processing helix chain 'y' and resid 31 through 42 Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 141 through 145 removed outlier: 3.824A pdb=" N GLY y 144 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 151 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain '3' and resid 132 through 135 Processing sheet with id=AA4, first strand: chain '5' and resid 33 through 36 removed outlier: 3.900A pdb=" N SER 5 338 " --> pdb=" O GLY 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 45 through 51 removed outlier: 5.037A pdb=" N PHE 5 47 " --> pdb=" O ALA 5 58 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA 5 58 " --> pdb=" O PHE 5 47 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG 5 59 " --> pdb=" O THR 5 63 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR 5 63 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 5 78 " --> pdb=" O CYS 5 66 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN 5 68 " --> pdb=" O LEU 5 76 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU 5 76 " --> pdb=" O ASN 5 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 92 through 97 removed outlier: 7.592A pdb=" N ALA 5 105 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET 5 95 " --> pdb=" O MET 5 103 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET 5 103 " --> pdb=" O MET 5 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 5 112 " --> pdb=" O LEU 5 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 132 through 135 removed outlier: 5.420A pdb=" N GLY 5 147 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP 5 151 " --> pdb=" O GLY 5 147 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE 5 180 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER 5 156 " --> pdb=" O LYS 5 178 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS 5 178 " --> pdb=" O SER 5 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 198 through 203 removed outlier: 4.588A pdb=" N GLY 5 200 " --> pdb=" O ILE 5 228 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN 5 233 " --> pdb=" O THR 5 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 256 through 262 removed outlier: 3.860A pdb=" N HIS 5 258 " --> pdb=" O ALA 5 271 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU 5 268 " --> pdb=" O PHE 5 280 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE 5 279 " --> pdb=" O ILE 5 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 5 286 " --> pdb=" O ASP 5 281 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 298 through 304 removed outlier: 4.019A pdb=" N GLY 5 312 " --> pdb=" O ASN 5 316 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN 5 316 " --> pdb=" O GLY 5 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.228A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 243 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.228A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 221 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU A 204 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 200 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 146 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 187 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 191 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL J 121 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU A 149 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.492A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 282 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.960A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.960A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 17 through 23 removed outlier: 6.037A pdb=" N GLU C 20 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 10 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 211 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.337A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 364 through 365 Processing sheet with id=AC1, first strand: chain 'E' and resid 94 through 97 removed outlier: 7.001A pdb=" N THR E 83 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.819A pdb=" N VAL F 84 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.653A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AC6, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AC7, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.867A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 130 through 132 removed outlier: 5.860A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL H 93 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE H 177 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'K' and resid 198 through 205 removed outlier: 6.115A pdb=" N VAL K 53 " --> pdb=" O CYS K 203 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 241 " --> pdb=" O PRO K 250 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AD3, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.924A pdb=" N ALA K 87 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE K 115 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU K 89 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.408A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD6, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD7, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.983A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 59 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 36 through 38 removed outlier: 7.534A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP N 120 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.114A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE2, first strand: chain 'P' and resid 15 through 22 removed outlier: 4.552A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'Q' and resid 121 through 123 removed outlier: 6.199A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 55 through 62 removed outlier: 5.140A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 87 through 95 removed outlier: 3.743A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 24 through 25 removed outlier: 5.981A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 86 through 88 Processing sheet with id=AE9, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF1, first strand: chain 'Y' and resid 66 through 67 removed outlier: 6.760A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 69 through 73 removed outlier: 7.173A pdb=" N LEU Y 80 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL Y 72 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU Y 78 " --> pdb=" O VAL Y 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 69 through 73 removed outlier: 4.627A pdb=" N LYS e 115 " --> pdb=" O TYR e 89 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.784A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER f 97 " --> pdb=" O HIS f 14 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AF6, first strand: chain 'o' and resid 131 through 134 removed outlier: 3.756A pdb=" N LYS o 179 " --> pdb=" O TYR o 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AF9, first strand: chain 'x' and resid 122 through 124 removed outlier: 5.958A pdb=" N LEU x 96 " --> pdb=" O GLU x 123 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU x 97 " --> pdb=" O LEU x 149 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU x 151 " --> pdb=" O LEU x 97 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR x 99 " --> pdb=" O LEU x 151 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU x 153 " --> pdb=" O THR x 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA x 160 " --> pdb=" O ASN x 152 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP x 154 " --> pdb=" O THR x 158 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR x 158 " --> pdb=" O ASP x 154 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET x 276 " --> pdb=" O TYR x 173 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR x 175 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU x 274 " --> pdb=" O THR x 175 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ARG x 275 " --> pdb=" O GLU x 292 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU x 292 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL x 277 " --> pdb=" O PHE x 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU x 288 " --> pdb=" O LYS x 279 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'x' and resid 177 through 180 removed outlier: 6.091A pdb=" N ASN x 178 " --> pdb=" O THR x 271 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR x 271 " --> pdb=" O ASN x 178 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG x 244 " --> pdb=" O LEU x 266 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE x 242 " --> pdb=" O PRO x 268 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE x 270 " --> pdb=" O LEU x 240 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU x 240 " --> pdb=" O PHE x 270 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'y' and resid 64 through 66 Processing sheet with id=AG3, first strand: chain 'y' and resid 152 through 153 2088 hydrogen bonds defined for protein. 5958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1148 hydrogen bonds 1842 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 883 stacking parallelities Total time for adding SS restraints: 65.47 Time building geometry restraints manager: 17.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14561 1.33 - 1.45: 29136 1.45 - 1.58: 36403 1.58 - 1.70: 3212 1.70 - 1.83: 160 Bond restraints: 83472 Sorted by residual: bond pdb=" CA ILE D 120 " pdb=" CB ILE D 120 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" C VAL 3 11 " pdb=" O VAL 3 11 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 7.07e+00 bond pdb=" CA MET Y 30 " pdb=" CB MET Y 30 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.76e-02 3.23e+03 4.52e+00 bond pdb=" CA ASP Q 90 " pdb=" C ASP Q 90 " ideal model delta sigma weight residual 1.528 1.505 0.022 1.33e-02 5.65e+03 2.81e+00 bond pdb=" O3' G 1 711 " pdb=" P U 1 712 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.50e-02 4.44e+03 2.70e+00 ... (remaining 83467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 120282 2.75 - 5.50: 532 5.50 - 8.25: 40 8.25 - 11.01: 4 11.01 - 13.76: 2 Bond angle restraints: 120860 Sorted by residual: angle pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta sigma weight residual 110.65 104.61 6.04 1.04e+00 9.25e-01 3.37e+01 angle pdb=" N LYS 4 46 " pdb=" CA LYS 4 46 " pdb=" C LYS 4 46 " ideal model delta sigma weight residual 111.07 105.19 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" O3' U 11159 " pdb=" C3' U 11159 " pdb=" C2' U 11159 " ideal model delta sigma weight residual 109.50 116.67 -7.17 1.50e+00 4.44e-01 2.29e+01 angle pdb=" CB MET D 439 " pdb=" CG MET D 439 " pdb=" SD MET D 439 " ideal model delta sigma weight residual 112.70 126.46 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" O3' A 1 488 " pdb=" C3' A 1 488 " pdb=" C2' A 1 488 " ideal model delta sigma weight residual 109.50 116.26 -6.76 1.50e+00 4.44e-01 2.03e+01 ... (remaining 120855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 47168 35.64 - 71.27: 4580 71.27 - 106.91: 478 106.91 - 142.55: 16 142.55 - 178.19: 19 Dihedral angle restraints: 52261 sinusoidal: 34358 harmonic: 17903 Sorted by residual: dihedral pdb=" O4' U 13314 " pdb=" C1' U 13314 " pdb=" N1 U 13314 " pdb=" C2 U 13314 " ideal model delta sinusoidal sigma weight residual -160.00 7.50 -167.50 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' U 13153 " pdb=" C1' U 13153 " pdb=" N1 U 13153 " pdb=" C2 U 13153 " ideal model delta sinusoidal sigma weight residual 200.00 54.37 145.63 1 1.50e+01 4.44e-03 7.79e+01 dihedral pdb=" O4' U 1 761 " pdb=" C1' U 1 761 " pdb=" N1 U 1 761 " pdb=" C2 U 1 761 " ideal model delta sinusoidal sigma weight residual -128.00 50.05 -178.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 52258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 13855 0.066 - 0.132: 1166 0.132 - 0.197: 62 0.197 - 0.263: 7 0.263 - 0.329: 2 Chirality restraints: 15092 Sorted by residual: chirality pdb=" C3' A 1 488 " pdb=" C4' A 1 488 " pdb=" O3' A 1 488 " pdb=" C2' A 1 488 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' U 11159 " pdb=" C4' U 11159 " pdb=" O3' U 11159 " pdb=" C2' U 11159 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C3' U 1 706 " pdb=" C4' U 1 706 " pdb=" O3' U 1 706 " pdb=" C2' U 1 706 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 15089 not shown) Planarity restraints: 9549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 4 173 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO 4 174 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO 4 174 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 4 174 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 46 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ILE L 46 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE L 46 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA L 47 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 414 " -0.024 2.00e-02 2.50e+03 1.16e-02 4.05e+00 pdb=" N9 G 1 414 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G 1 414 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 1 414 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 1 414 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 1 414 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G 1 414 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G 1 414 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 1 414 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 1 414 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 414 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 1 414 " 0.003 2.00e-02 2.50e+03 ... (remaining 9546 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 3344 2.67 - 3.23: 73594 3.23 - 3.78: 149434 3.78 - 4.34: 196484 4.34 - 4.90: 276450 Nonbonded interactions: 699306 Sorted by model distance: nonbonded pdb=" OP2 A 13367 " pdb=" N6 A 13368 " model vdw 2.108 3.120 nonbonded pdb=" OH TYR 3 86 " pdb=" OG1 THR 3 113 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR C 267 " pdb=" OE1 GLU C 281 " model vdw 2.198 3.040 nonbonded pdb=" N2 G 11416 " pdb=" O GLY C 243 " model vdw 2.203 3.120 nonbonded pdb=" O2' A 11012 " pdb=" O4' U 11013 " model vdw 2.204 3.040 ... (remaining 699301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 8.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.600 Check model and map are aligned: 0.450 Set scattering table: 0.590 Process input model: 201.600 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.300 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: 0.030 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.004 0.055 83472 Z= 0.289 Angle : 0.555 13.756 120860 Z= 0.296 Chirality : 0.036 0.329 15092 Planarity : 0.004 0.063 9549 Dihedral : 22.511 178.186 40597 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 0.40 % Allowed : 22.54 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.11 (0.11), residues: 6040 helix: 0.78 (0.11), residues: 2286 sheet: -0.07 (0.19), residues: 860 loop : -0.71 (0.12), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 5 80 HIS 0.006 0.001 HIS C 314 PHE 0.023 0.001 PHE D 143 TYR 0.026 0.002 TYR E 86 ARG 0.011 0.001 ARG e 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 362 time to evaluate : 4.854 Fit side-chains revert: symmetry clash REVERT: i 44 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7131 (tm-30) REVERT: x 218 LEU cc_start: 0.8559 (tp) cc_final: 0.8349 (tp) outliers start: 14 outliers final: 5 residues processed: 367 average time/residue: 0.8023 time to fit residues: 511.4509 Evaluate side-chains 344 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 339 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 2.9990 chunk 576 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 388 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 595 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 362 optimal weight: 3.9990 chunk 443 optimal weight: 9.9990 chunk 690 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 191 ASN 5 292 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 HIS e 96 ASN h 19 GLN h 21 GLN v 6 GLN v 33 ASN v 152 GLN x 159 ASN x 264 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 83472 Z= 0.475 Angle : 0.755 9.750 120860 Z= 0.376 Chirality : 0.044 0.345 15092 Planarity : 0.006 0.074 9549 Dihedral : 22.994 179.384 31573 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 3.65 % Allowed : 22.60 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.19 (0.11), residues: 6040 helix: 0.82 (0.11), residues: 2365 sheet: -0.18 (0.19), residues: 832 loop : -0.87 (0.12), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP 4 76 HIS 0.008 0.002 HIS C 314 PHE 0.021 0.002 PHE x 290 TYR 0.025 0.002 TYR 4 50 ARG 0.009 0.001 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 345 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6306 (ttp-170) REVERT: 3 104 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: 3 123 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7474 (ttp80) REVERT: 3 129 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6607 (m170) REVERT: 3 152 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.6984 (mm) REVERT: C 100 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.2974 (tpt170) REVERT: D 156 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: E 86 TYR cc_start: 0.4477 (OUTLIER) cc_final: 0.3215 (m-80) REVERT: F 247 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: Q 127 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: Q 131 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8578 (ttm170) REVERT: Y 80 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7295 (mm) REVERT: e 58 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8063 (mtpt) REVERT: e 96 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.7559 (p0) outliers start: 137 outliers final: 70 residues processed: 453 average time/residue: 0.7382 time to fit residues: 577.7477 Evaluate side-chains 398 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 314 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 123 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 152 LEU Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 121 ILE Chi-restraints excluded: chain 4 residue 134 VAL Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 152 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 25 GLN Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 135 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 188 LEU Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 7.9990 chunk 214 optimal weight: 0.0770 chunk 574 optimal weight: 50.0000 chunk 469 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 691 optimal weight: 20.0000 chunk 746 optimal weight: 30.0000 chunk 615 optimal weight: 1.9990 chunk 685 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 554 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 188 HIS D 213 ASN E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 83472 Z= 0.171 Angle : 0.560 8.254 120860 Z= 0.285 Chirality : 0.036 0.243 15092 Planarity : 0.004 0.049 9549 Dihedral : 22.788 179.670 31569 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.28 % Favored : 95.58 % Rotamer: Outliers : 2.98 % Allowed : 23.42 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.13 (0.11), residues: 6040 helix: 1.11 (0.11), residues: 2371 sheet: -0.10 (0.19), residues: 834 loop : -0.70 (0.12), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 407 HIS 0.005 0.001 HIS N 192 PHE 0.017 0.001 PHE A 248 TYR 0.016 0.001 TYR m 202 ARG 0.006 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 383 time to evaluate : 4.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.5980 (ttp-170) REVERT: 5 95 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6353 (ptp) REVERT: D 156 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: E 86 TYR cc_start: 0.4443 (OUTLIER) cc_final: 0.3126 (m-80) REVERT: F 247 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7005 (mt0) REVERT: v 166 TYR cc_start: 0.7431 (t80) cc_final: 0.7187 (t80) outliers start: 112 outliers final: 56 residues processed: 470 average time/residue: 0.7357 time to fit residues: 602.8063 Evaluate side-chains 402 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 341 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 94 SER Chi-restraints excluded: chain 5 residue 95 MET Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 261 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 8.9990 chunk 519 optimal weight: 10.0000 chunk 358 optimal weight: 0.0060 chunk 76 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 464 optimal weight: 50.0000 chunk 693 optimal weight: 0.5980 chunk 734 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 657 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 117 GLN ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN P 101 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 ASN ** m 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 6 GLN v 152 GLN x 50 ASN x 221 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 83472 Z= 0.238 Angle : 0.581 9.003 120860 Z= 0.294 Chirality : 0.037 0.261 15092 Planarity : 0.004 0.050 9549 Dihedral : 22.713 178.682 31569 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.79 % Favored : 95.06 % Rotamer: Outliers : 3.51 % Allowed : 23.88 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.18 (0.11), residues: 6040 helix: 1.19 (0.11), residues: 2365 sheet: -0.11 (0.19), residues: 836 loop : -0.68 (0.12), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 120 HIS 0.004 0.001 HIS N 192 PHE 0.029 0.001 PHE D 143 TYR 0.017 0.001 TYR 3 118 ARG 0.006 0.000 ARG h 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 352 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6163 (ttp-170) REVERT: 3 129 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6585 (m170) REVERT: 4 93 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7285 (ptt90) REVERT: 4 212 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3600 (p90) REVERT: C 100 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.2678 (tpt170) REVERT: D 156 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: E 86 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.3111 (m-80) REVERT: F 247 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: Y 80 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7480 (mm) outliers start: 132 outliers final: 80 residues processed: 455 average time/residue: 0.7563 time to fit residues: 595.9912 Evaluate side-chains 422 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 333 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 93 ARG Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 121 ILE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 52 GLU Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 94 SER Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 0.8980 chunk 417 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 546 optimal weight: 0.5980 chunk 303 optimal weight: 0.8980 chunk 626 optimal weight: 7.9990 chunk 507 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 375 optimal weight: 4.9990 chunk 659 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 71 HIS ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS v 6 GLN v 152 GLN ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 83472 Z= 0.150 Angle : 0.530 9.583 120860 Z= 0.269 Chirality : 0.035 0.242 15092 Planarity : 0.004 0.049 9549 Dihedral : 22.604 178.705 31569 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % Rotamer: Outliers : 3.25 % Allowed : 23.74 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.36 (0.11), residues: 6040 helix: 1.35 (0.11), residues: 2370 sheet: -0.04 (0.19), residues: 803 loop : -0.58 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 4 76 HIS 0.010 0.001 HIS 5 51 PHE 0.031 0.001 PHE D 143 TYR 0.017 0.001 TYR F 143 ARG 0.004 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 375 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.5914 (ttp-170) REVERT: D 156 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: D 343 MET cc_start: 0.6439 (ptp) cc_final: 0.5952 (ptp) REVERT: E 86 TYR cc_start: 0.4071 (OUTLIER) cc_final: 0.2761 (m-80) REVERT: Y 16 LYS cc_start: 0.8011 (tttp) cc_final: 0.7709 (tttt) REVERT: i 43 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6279 (tpm170) outliers start: 122 outliers final: 75 residues processed: 468 average time/residue: 0.7493 time to fit residues: 609.3456 Evaluate side-chains 424 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 345 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 7 ILE Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain x residue 261 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 4.9990 chunk 661 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 431 optimal weight: 10.0000 chunk 181 optimal weight: 0.0670 chunk 735 optimal weight: 8.9990 chunk 610 optimal weight: 0.0670 chunk 340 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 243 optimal weight: 40.0000 chunk 386 optimal weight: 0.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 61 ASN v 6 GLN v 152 GLN x 221 GLN ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 83472 Z= 0.247 Angle : 0.576 9.666 120860 Z= 0.292 Chirality : 0.037 0.270 15092 Planarity : 0.004 0.052 9549 Dihedral : 22.575 178.804 31567 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 4.05 % Allowed : 23.61 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.33 (0.11), residues: 6040 helix: 1.35 (0.11), residues: 2364 sheet: -0.10 (0.19), residues: 817 loop : -0.60 (0.12), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 4 76 HIS 0.008 0.001 HIS 5 51 PHE 0.031 0.001 PHE D 143 TYR 0.018 0.002 TYR Q 32 ARG 0.008 0.000 ARG h 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 355 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6178 (ttp-170) REVERT: 3 129 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6555 (m170) REVERT: 4 212 TYR cc_start: 0.4922 (OUTLIER) cc_final: 0.3540 (p90) REVERT: 5 95 MET cc_start: 0.5889 (ptt) cc_final: 0.5381 (ptt) REVERT: C 100 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.2676 (tpt170) REVERT: D 156 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: D 343 MET cc_start: 0.6220 (ptp) cc_final: 0.5874 (ptp) REVERT: E 86 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.2989 (m-80) REVERT: P 54 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6585 (m90) REVERT: Q 127 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: S 175 PHE cc_start: 0.4772 (OUTLIER) cc_final: 0.4328 (t80) REVERT: i 18 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7675 (mtp-110) REVERT: i 43 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6234 (tpm170) outliers start: 152 outliers final: 95 residues processed: 476 average time/residue: 0.7572 time to fit residues: 626.9978 Evaluate side-chains 441 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 335 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 253 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 278 SER Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 188 LEU Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain x residue 261 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 418 optimal weight: 10.0000 chunk 536 optimal weight: 0.0030 chunk 416 optimal weight: 0.7980 chunk 618 optimal weight: 4.9990 chunk 410 optimal weight: 0.6980 chunk 732 optimal weight: 6.9990 chunk 458 optimal weight: 20.0000 chunk 446 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 71 HIS ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 HIS 5 233 GLN 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS x 221 GLN ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 83472 Z= 0.255 Angle : 0.582 11.937 120860 Z= 0.295 Chirality : 0.038 0.268 15092 Planarity : 0.004 0.064 9549 Dihedral : 22.552 179.081 31567 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.79 % Favored : 95.06 % Rotamer: Outliers : 3.97 % Allowed : 23.90 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.32 (0.11), residues: 6040 helix: 1.37 (0.11), residues: 2366 sheet: -0.17 (0.19), residues: 830 loop : -0.61 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 4 76 HIS 0.008 0.001 HIS 3 106 PHE 0.023 0.001 PHE N 21 TYR 0.023 0.002 TYR 3 118 ARG 0.017 0.000 ARG t 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 356 time to evaluate : 5.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6177 (ttp-170) REVERT: 3 129 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6561 (m170) REVERT: 4 24 GLU cc_start: 0.7477 (mp0) cc_final: 0.7208 (mp0) REVERT: 4 212 TYR cc_start: 0.4975 (OUTLIER) cc_final: 0.3640 (p90) REVERT: 5 95 MET cc_start: 0.5845 (ptt) cc_final: 0.5414 (ptt) REVERT: C 100 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.2671 (tpt170) REVERT: D 156 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: D 343 MET cc_start: 0.6136 (ptp) cc_final: 0.5835 (ptp) REVERT: E 86 TYR cc_start: 0.4342 (OUTLIER) cc_final: 0.3023 (m-80) REVERT: P 54 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6521 (m90) REVERT: Q 127 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: S 175 PHE cc_start: 0.4927 (OUTLIER) cc_final: 0.4453 (t80) REVERT: e 58 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8131 (mtpt) REVERT: f 30 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8712 (mm) REVERT: i 18 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7728 (mtp-110) outliers start: 149 outliers final: 105 residues processed: 471 average time/residue: 0.7369 time to fit residues: 606.6661 Evaluate side-chains 457 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 340 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 52 GLU Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 127 HIS Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 278 SER Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 135 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 64 THR Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain x residue 261 THR Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 152 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 20.0000 chunk 292 optimal weight: 0.6980 chunk 437 optimal weight: 50.0000 chunk 220 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 50.0000 chunk 465 optimal weight: 50.0000 chunk 499 optimal weight: 0.9990 chunk 362 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 575 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 HIS 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN x 221 GLN ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 83472 Z= 0.236 Angle : 0.574 9.475 120860 Z= 0.291 Chirality : 0.037 0.259 15092 Planarity : 0.004 0.054 9549 Dihedral : 22.515 179.461 31567 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.08 % Rotamer: Outliers : 3.73 % Allowed : 24.33 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.35 (0.11), residues: 6040 helix: 1.38 (0.11), residues: 2373 sheet: -0.24 (0.19), residues: 842 loop : -0.57 (0.12), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 4 76 HIS 0.016 0.001 HIS T 152 PHE 0.037 0.001 PHE D 143 TYR 0.019 0.002 TYR 4 183 ARG 0.017 0.000 ARG t 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 354 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6178 (ttp-170) REVERT: 3 129 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6544 (m170) REVERT: 4 142 MET cc_start: 0.7113 (mmp) cc_final: 0.6831 (mmp) REVERT: 4 212 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.3714 (p90) REVERT: 5 95 MET cc_start: 0.5767 (ptt) cc_final: 0.5417 (ptt) REVERT: 5 127 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6615 (m90) REVERT: C 100 ARG cc_start: 0.4892 (OUTLIER) cc_final: 0.2648 (tpt170) REVERT: D 156 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: D 343 MET cc_start: 0.6078 (ptp) cc_final: 0.5817 (ptp) REVERT: E 86 TYR cc_start: 0.4569 (OUTLIER) cc_final: 0.3276 (m-80) REVERT: P 54 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6515 (m90) REVERT: Q 127 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: S 175 PHE cc_start: 0.4886 (OUTLIER) cc_final: 0.4460 (t80) REVERT: e 58 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8122 (mtpt) REVERT: f 30 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8747 (mm) REVERT: i 18 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: i 43 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6212 (tpm170) REVERT: j 25 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.7015 (ttp-170) outliers start: 140 outliers final: 111 residues processed: 460 average time/residue: 0.7436 time to fit residues: 598.1977 Evaluate side-chains 469 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 344 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 94 SER Chi-restraints excluded: chain 5 residue 127 HIS Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 253 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 278 SER Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 135 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 64 THR Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 221 GLN Chi-restraints excluded: chain x residue 232 THR Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain x residue 261 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 50.0000 chunk 701 optimal weight: 0.9990 chunk 640 optimal weight: 0.9980 chunk 682 optimal weight: 50.0000 chunk 410 optimal weight: 0.0770 chunk 297 optimal weight: 0.6980 chunk 536 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 616 optimal weight: 3.9990 chunk 645 optimal weight: 5.9990 chunk 680 optimal weight: 4.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS v 152 GLN x 221 GLN ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 83472 Z= 0.202 Angle : 0.554 12.784 120860 Z= 0.282 Chirality : 0.036 0.245 15092 Planarity : 0.004 0.055 9549 Dihedral : 22.448 179.489 31567 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.49 % Rotamer: Outliers : 3.62 % Allowed : 24.43 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.41 (0.11), residues: 6040 helix: 1.44 (0.11), residues: 2368 sheet: -0.19 (0.19), residues: 836 loop : -0.54 (0.12), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 4 76 HIS 0.021 0.001 HIS 5 127 PHE 0.037 0.001 PHE D 143 TYR 0.017 0.001 TYR 3 118 ARG 0.014 0.000 ARG t 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 358 time to evaluate : 4.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6046 (ttp-170) REVERT: 3 129 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6546 (m170) REVERT: 4 142 MET cc_start: 0.7086 (mmp) cc_final: 0.6811 (mmp) REVERT: 4 212 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.3766 (p90) REVERT: 5 95 MET cc_start: 0.5870 (ptt) cc_final: 0.5505 (ptt) REVERT: C 100 ARG cc_start: 0.4832 (OUTLIER) cc_final: 0.2627 (tpt170) REVERT: D 156 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: D 343 MET cc_start: 0.6017 (ptp) cc_final: 0.5794 (ptp) REVERT: E 86 TYR cc_start: 0.4547 (OUTLIER) cc_final: 0.3409 (m-80) REVERT: S 175 PHE cc_start: 0.4810 (OUTLIER) cc_final: 0.4372 (t80) REVERT: f 30 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8758 (mm) REVERT: i 18 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7712 (mtp180) REVERT: i 43 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6233 (tpm170) outliers start: 136 outliers final: 112 residues processed: 463 average time/residue: 0.7326 time to fit residues: 590.8416 Evaluate side-chains 459 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 337 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 253 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 278 SER Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 7 ILE Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 135 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 64 THR Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 221 GLN Chi-restraints excluded: chain x residue 232 THR Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain x residue 261 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 50.0000 chunk 721 optimal weight: 6.9990 chunk 440 optimal weight: 8.9990 chunk 342 optimal weight: 9.9990 chunk 501 optimal weight: 0.7980 chunk 757 optimal weight: 6.9990 chunk 696 optimal weight: 3.9990 chunk 602 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 465 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 188 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 252 GLN ** v 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN ** x 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 83472 Z= 0.414 Angle : 0.702 12.804 120860 Z= 0.352 Chirality : 0.042 0.329 15092 Planarity : 0.005 0.061 9549 Dihedral : 22.539 179.354 31567 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.15 % Rotamer: Outliers : 3.51 % Allowed : 24.86 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.15 (0.11), residues: 6040 helix: 1.22 (0.11), residues: 2376 sheet: -0.21 (0.19), residues: 821 loop : -0.73 (0.12), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP 5 171 HIS 0.011 0.002 HIS 3 106 PHE 0.035 0.002 PHE D 143 TYR 0.027 0.002 TYR 4 50 ARG 0.013 0.001 ARG t 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 333 time to evaluate : 4.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6372 (ttp-170) REVERT: 3 129 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6676 (m170) REVERT: 4 142 MET cc_start: 0.7188 (mmp) cc_final: 0.6931 (mmp) REVERT: 4 212 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.3784 (p90) REVERT: 5 95 MET cc_start: 0.5924 (ptt) cc_final: 0.5565 (ptt) REVERT: C 100 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.2944 (tpt170) REVERT: D 156 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: E 86 TYR cc_start: 0.4736 (OUTLIER) cc_final: 0.3626 (m-80) REVERT: F 110 MET cc_start: 0.8133 (mtp) cc_final: 0.7862 (mtm) REVERT: Q 127 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: S 175 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.4431 (t80) REVERT: e 58 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8172 (mtpt) REVERT: f 30 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8603 (mm) REVERT: i 18 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7612 (mtp-110) REVERT: i 43 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6424 (tpm170) outliers start: 132 outliers final: 110 residues processed: 437 average time/residue: 0.7476 time to fit residues: 569.4777 Evaluate side-chains 446 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 324 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 94 SER Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 253 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 278 SER Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 135 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 64 THR Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 232 THR Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain x residue 261 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 30.0000 chunk 642 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 555 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 603 optimal weight: 50.0000 chunk 252 optimal weight: 9.9990 chunk 620 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 106 HIS ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 282 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 188 HIS D 225 HIS E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS v 152 GLN ** x 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.153376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.136846 restraints weight = 231340.833| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.49 r_work: 0.3984 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 83472 Z= 0.231 Angle : 0.580 12.715 120860 Z= 0.294 Chirality : 0.037 0.252 15092 Planarity : 0.004 0.058 9549 Dihedral : 22.458 179.512 31567 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 3.30 % Allowed : 25.02 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.29 (0.11), residues: 6040 helix: 1.36 (0.11), residues: 2376 sheet: -0.23 (0.19), residues: 827 loop : -0.64 (0.12), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 4 76 HIS 0.009 0.001 HIS 5 51 PHE 0.036 0.001 PHE D 143 TYR 0.017 0.002 TYR S 42 ARG 0.012 0.000 ARG t 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13656.64 seconds wall clock time: 243 minutes 3.98 seconds (14583.98 seconds total)