Starting phenix.real_space_refine (version: dev) on Fri Dec 16 05:12:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev3_24421/12_2022/8ev3_24421.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev3_24421/12_2022/8ev3_24421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev3_24421/12_2022/8ev3_24421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev3_24421/12_2022/8ev3_24421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev3_24421/12_2022/8ev3_24421.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev3_24421/12_2022/8ev3_24421.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "4 GLU 37": "OE1" <-> "OE2" Residue "5 GLU 88": "OE1" <-> "OE2" Residue "5 GLU 134": "OE1" <-> "OE2" Residue "5 TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "N GLU 9": "OE1" <-> "OE2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 153": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "h GLU 7": "OE1" <-> "OE2" Residue "t GLU 55": "OE1" <-> "OE2" Residue "t GLU 67": "OE1" <-> "OE2" Residue "v GLU 136": "OE1" <-> "OE2" Residue "v GLU 142": "OE1" <-> "OE2" Residue "v GLU 177": "OE1" <-> "OE2" Residue "x GLU 89": "OE1" <-> "OE2" Residue "x GLU 297": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 84746 Number of models: 1 Model: "" Number of chains: 42 Chain: "1" Number of atoms: 31076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 31076 Classifications: {'RNA': 1452} Modifications used: {'rna2p_pur': 149, 'rna2p_pyr': 101, 'rna3p_pur': 665, 'rna3p_pyr': 537} Link IDs: {'rna2p': 249, 'rna3p': 1202} Chain breaks: 25 Chain: "2" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3189 Classifications: {'RNA': 150} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 61} Link IDs: {'rna2p': 26, 'rna3p': 123} Chain breaks: 2 Chain: "3" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1596 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "4" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1776 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "5" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2686 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "6" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 16, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 30, 'rna3p': 44} Chain breaks: 3 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1999 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain breaks: 1 Chain: "B" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2641 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2810 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 343} Chain: "D" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3186 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 71 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: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1944 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 228} Chain: "G" Number of atoms: 1273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1265 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1265 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 bond proxies already assigned to first conformer: 1274 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 902 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 4, 'TRANS': 178} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 288 Chain: "J" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 459 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "K" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1914 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 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: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} 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: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1478 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain breaks: 1 Chain: "P" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1164 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 1 Chain: "Q" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1047 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 129} 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: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 446 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 123 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: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 317 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 63} Chain breaks: 3 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 119 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: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 615 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain breaks: 1 Chain: "n" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 1791 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 342} Chain breaks: 2 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1231 Unresolved non-hydrogen angles: 1571 Unresolved non-hydrogen dihedrals: 1059 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 9, 'TYR:plan': 20, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 25, 'GLU:plan': 21, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 677 Chain: "o" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1026 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 130} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "r" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 283 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 7 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: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1008 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 437 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 267 Chain: "u" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 377 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 156 Chain: "v" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 1 Chain: "x" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2516 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 293} Chain: "y" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 925 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 515 Unresolved non-hydrogen angles: 673 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 281 Chain: "T" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 147 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} 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 74241 SG CYS j 19 89.479 91.665 164.517 1.00 24.99 S ATOM 74269 SG CYS j 22 91.932 92.623 161.732 1.00 25.18 S ATOM 74365 SG CYS j 34 90.746 89.071 161.977 1.00 17.42 S ATOM 74382 SG CYS j 37 93.024 90.549 164.718 1.00 31.32 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP G 227 " occ=0.46 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.54 Time building chain proxies: 36.93, per 1000 atoms: 0.44 Number of scatterers: 84746 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 124 16.00 P 1677 15.00 O 20456 8.00 N 15649 7.00 C 46839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.17 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " Number of angles added : 6 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12484 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 70 sheets defined 43.1% alpha, 16.6% beta 507 base pairs and 950 stacking pairs defined. Time for finding SS restraints: 30.24 Creating SS restraints... Processing helix chain '3' and resid 3 through 14 removed outlier: 3.630A pdb=" N HIS 3 13 " --> pdb=" O GLN 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 70 Processing helix chain '3' and resid 72 through 75 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: 3.744A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 171 Processing helix chain '3' and resid 182 through 194 Processing helix chain '4' and resid 7 through 12 Processing helix chain '4' and resid 15 through 30 removed outlier: 4.055A pdb=" N ARG 4 28 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE 4 29 " --> pdb=" O SER 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 54 removed outlier: 3.511A pdb=" N GLY 4 47 " --> pdb=" O LYS 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 71 Processing helix chain '4' and resid 79 through 94 Processing helix chain '4' and resid 102 through 128 removed outlier: 3.524A pdb=" N LEU 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU 4 109 " --> pdb=" O LYS 4 105 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE 4 118 " --> pdb=" O CYS 4 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS 4 126 " --> pdb=" O GLN 4 122 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR 4 127 " --> pdb=" O THR 4 123 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 144 removed outlier: 3.511A pdb=" N VAL 4 133 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) Processing helix chain '4' and resid 154 through 173 removed outlier: 3.864A pdb=" N LEU 4 158 " --> pdb=" O PRO 4 154 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR 4 166 " --> pdb=" O ALA 4 162 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU 4 167 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 4 171 " --> pdb=" O GLU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 192 Processing helix chain '4' and resid 195 through 206 Proline residue: 4 203 - end of helix Processing helix chain '5' and resid 40 through 43 removed outlier: 3.535A pdb=" N LYS 5 43 " --> pdb=" O ASP 5 40 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 40 through 43' Processing helix chain '5' and resid 83 through 87 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.602A pdb=" N SER A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 4.044A pdb=" N GLU A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.985A pdb=" N ASP A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 4.273A 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 250 through 264 removed outlier: 3.610A pdb=" N ARG A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.871A pdb=" N ASN A 292 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.591A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 140 through 154 removed outlier: 4.109A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.530A 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 'B' and resid 372 through 380 removed outlier: 3.632A pdb=" N ALA B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.876A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.718A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' 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 259 Processing helix chain 'C' and resid 259 through 265 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 98 through 107 Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.628A pdb=" N ARG D 118 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.635A 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 200 through 211 removed outlier: 3.708A pdb=" N LYS D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 229 removed outlier: 3.513A pdb=" N LEU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 279 through 290 Processing helix chain 'D' and resid 322 through 334 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 removed outlier: 3.713A pdb=" N HIS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 425 " --> pdb=" O ILE D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 446 through 455 removed outlier: 4.168A pdb=" N ARG D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 451 " --> pdb=" O GLY D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 483 through 503 Processing helix chain 'D' and resid 516 through 524 Processing helix chain 'E' and resid 120 through 125 removed outlier: 3.595A pdb=" N PHE E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.585A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 162 " --> pdb=" O LYS E 158 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 3.972A 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: 3.663A pdb=" N SER F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.631A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.898A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (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 198 Processing helix chain 'F' and resid 201 through 209 removed outlier: 3.534A pdb=" N LEU F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 247 removed outlier: 4.351A pdb=" N GLY F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 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 removed outlier: 3.589A pdb=" N LEU G 93 " --> pdb=" O GLN G 89 " (cutoff:3.500A) 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 118 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 182 through 190 removed outlier: 3.520A pdb=" N VAL G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) 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 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: 3.829A 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 185 Processing helix chain 'K' and resid 14 through 27 removed outlier: 3.713A pdb=" N GLU K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG K 27 " --> pdb=" O TYR K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 105 removed outlier: 4.322A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.617A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 136 Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 155 through 160 removed outlier: 3.543A pdb=" N TYR K 159 " --> pdb=" O GLY K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 187 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'K' and resid 231 through 234 removed outlier: 4.118A pdb=" N LYS K 234 " --> pdb=" O ASP K 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 231 through 234' Processing helix chain 'K' and resid 256 through 265 Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.268A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.545A pdb=" N LEU L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 22 removed outlier: 4.349A pdb=" N TYR M 21 " --> pdb=" O LYS M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 105 removed outlier: 3.523A pdb=" N GLN M 104 " --> pdb=" O LYS M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 removed outlier: 3.548A pdb=" N GLU M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.579A pdb=" N MET N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 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 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 159 through 163 removed outlier: 3.582A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 189 through 193 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 60 Processing helix chain 'O' and resid 76 through 88 removed outlier: 3.590A pdb=" N MET O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 110 through 115 removed outlier: 3.946A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 150 through 186 removed outlier: 3.687A pdb=" N LYS O 178 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE O 179 " --> pdb=" O LYS O 175 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 192 removed outlier: 4.298A pdb=" N GLN O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 196 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.532A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 71 through 77 removed outlier: 4.169A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 106 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.702A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'S' and resid 32 through 47 Processing helix chain 'S' and resid 97 through 114 Processing helix chain 'S' and resid 136 through 142 Processing helix chain 'V' and resid 122 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: 4.574A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'b' and resid 15 through 28 Processing helix chain 'b' and resid 42 through 61 Processing helix chain 'b' and resid 123 through 143 Processing helix chain 'e' and resid 37 through 42 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.571A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU e 81 " --> pdb=" O SER e 77 " (cutoff:3.500A) 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 112 removed outlier: 3.924A pdb=" N GLU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA e 111 " --> pdb=" O GLU e 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 43 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: 3.665A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.634A pdb=" N LEU h 20 " --> pdb=" O LEU h 16 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN h 21 " --> pdb=" O ALA h 17 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 3.526A pdb=" N LYS h 51 " --> pdb=" O LYS h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 47 Processing helix chain 'i' and resid 49 through 61 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 56 Processing helix chain 'j' and resid 64 through 74 removed outlier: 3.520A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) Processing helix chain 'm' and resid 221 through 226 removed outlier: 3.588A pdb=" N ARG m 224 " --> pdb=" O PRO m 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA m 226 " --> pdb=" O ARG m 223 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 249 through 258 removed outlier: 3.563A pdb=" N GLU m 255 " --> pdb=" O GLU m 251 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 15 Processing helix chain 'n' and resid 19 through 27 Processing helix chain 'n' and resid 29 through 40 Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 66 through 74 removed outlier: 4.303A pdb=" N HIS n 74 " --> pdb=" O GLN n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 98 removed outlier: 4.349A pdb=" N GLN n 79 " --> pdb=" O GLU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 109 removed outlier: 3.584A pdb=" N ALA n 103 " --> pdb=" O GLU n 99 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA n 108 " --> pdb=" O LYS n 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG n 109 " --> pdb=" O ARG n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 123 Processing helix chain 'n' and resid 125 through 132 Processing helix chain 'n' and resid 132 through 146 removed outlier: 4.313A pdb=" N ALA n 136 " --> pdb=" O ASP n 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR n 145 " --> pdb=" O PHE n 141 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET n 146 " --> pdb=" O LEU n 142 " (cutoff:3.500A) Processing helix chain 'n' and resid 153 through 175 Processing helix chain 'n' and resid 215 through 242 Processing helix chain 'n' and resid 250 through 256 Processing helix chain 'n' and resid 257 through 261 removed outlier: 6.594A pdb=" N LEU n 260 " --> pdb=" O ALA n 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 365 through 376 removed outlier: 3.678A pdb=" N PHE n 371 " --> pdb=" O PHE n 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 420 through 431 removed outlier: 3.583A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 129 removed outlier: 4.204A pdb=" N GLN o 127 " --> pdb=" O MET o 123 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 166 Processing helix chain 'o' and resid 182 through 186 Processing helix chain 'o' and resid 187 through 192 removed outlier: 4.221A pdb=" N PHE o 191 " --> pdb=" O GLU o 188 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS o 192 " --> pdb=" O ASN o 189 " (cutoff:3.500A) 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 4 through 14 Processing helix chain 'r' and resid 17 through 42 removed outlier: 3.713A pdb=" N GLU r 21 " --> pdb=" O ARG r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 59 Processing helix chain 't' and resid 53 through 76 removed outlier: 3.632A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 102 through 112 Processing helix chain 't' and resid 126 through 136 Processing helix chain 't' and resid 146 through 158 Processing helix chain 't' and resid 171 through 179 removed outlier: 4.020A pdb=" N ILE t 175 " --> pdb=" O ASP t 171 " (cutoff:3.500A) Processing helix chain 't' and resid 186 through 197 Processing helix chain 't' and resid 200 through 208 Processing helix chain 't' and resid 239 through 249 removed outlier: 3.723A pdb=" N GLU t 243 " --> pdb=" O GLU t 239 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.615A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 83 through 93 Processing helix chain 'v' and resid 3 through 12 removed outlier: 3.572A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 53 Processing helix chain 'v' and resid 120 through 125 Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.735A pdb=" N LYS v 173 " --> pdb=" O ARG v 169 " (cutoff:3.500A) Processing helix chain 'v' and resid 179 through 184 Processing helix chain 'v' and resid 194 through 207 removed outlier: 3.588A pdb=" N ALA v 207 " --> pdb=" O ILE v 203 " (cutoff:3.500A) Processing helix chain 'x' and resid 6 through 39 removed outlier: 3.748A pdb=" N ASP x 39 " --> pdb=" O GLU x 35 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 50 removed outlier: 3.858A pdb=" N LYS x 43 " --> pdb=" O ASP x 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG x 46 " --> pdb=" O LYS x 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER x 48 " --> pdb=" O ARG x 44 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 78 Processing helix chain 'x' and resid 83 through 88 removed outlier: 3.728A pdb=" N PHE x 87 " --> pdb=" O PHE x 83 " (cutoff:3.500A) Processing helix chain 'x' and resid 105 through 119 removed outlier: 3.548A pdb=" N CYS x 118 " --> pdb=" O GLU x 114 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE x 119 " --> pdb=" O LEU x 115 " (cutoff:3.500A) Processing helix chain 'x' and resid 132 through 142 removed outlier: 3.765A pdb=" N LYS x 142 " --> pdb=" O GLU x 138 " (cutoff:3.500A) Processing helix chain 'x' and resid 181 through 185 Processing helix chain 'x' and resid 205 through 217 removed outlier: 3.507A pdb=" N THR x 210 " --> pdb=" O ARG x 206 " (cutoff:3.500A) Processing helix chain 'x' and resid 296 through 300 removed outlier: 3.669A pdb=" N ASP x 300 " --> pdb=" O GLU x 297 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 Processing helix chain 'y' and resid 31 through 40 Processing helix chain 'y' and resid 52 through 56 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 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 185 through 190 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 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 56 Processing sheet with id=AA3, first strand: chain '3' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain '5' and resid 34 through 37 removed outlier: 4.434A pdb=" N GLN 5 11 " --> pdb=" O ASP 5 7 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS 5 2 " --> pdb=" O ILE 5 342 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY 5 6 " --> pdb=" O SER 5 338 " (cutoff:3.500A) removed outlier: 3.641A 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 47 removed outlier: 6.616A pdb=" N ALA 5 58 " --> pdb=" O LEU 5 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 45 through 47 removed outlier: 6.616A pdb=" N ALA 5 58 " --> pdb=" O LEU 5 46 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG 5 59 " --> pdb=" O THR 5 63 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR 5 63 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN 5 68 " --> pdb=" O LEU 5 76 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU 5 76 " --> pdb=" O ASN 5 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain '5' and resid 132 through 135 removed outlier: 5.370A pdb=" N GLY 5 147 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP 5 151 " --> pdb=" O GLY 5 147 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER 5 156 " --> pdb=" O LYS 5 178 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS 5 178 " --> pdb=" O SER 5 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 198 through 203 removed outlier: 3.789A pdb=" N PHE 5 225 " --> pdb=" O TYR 5 237 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN 5 233 " --> pdb=" O THR 5 229 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP 5 238 " --> pdb=" O PRO 5 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 256 through 262 removed outlier: 6.518A pdb=" N ALA 5 271 " --> pdb=" O SER 5 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL 5 259 " --> pdb=" O TYR 5 269 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR 5 269 " --> pdb=" O VAL 5 259 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU 5 261 " --> pdb=" O LEU 5 267 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU 5 267 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU 5 268 " --> pdb=" O PHE 5 280 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN 5 276 " --> pdb=" O ASP 5 272 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE 5 279 " --> pdb=" O ILE 5 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 298 through 304 removed outlier: 3.734A pdb=" N VAL 5 307 " --> pdb=" O LEU 5 304 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY 5 312 " --> pdb=" O ASN 5 316 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN 5 316 " --> pdb=" O GLY 5 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 71 through 77 removed outlier: 5.339A pdb=" N SER A 49 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 76 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER A 50 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 121 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 232 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 123 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 192 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 77 removed outlier: 5.339A pdb=" N SER A 49 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 76 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER A 50 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 121 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 232 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 123 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE A 230 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS A 244 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 232 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.867A pdb=" N ALA B 162 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.867A pdb=" N ALA B 162 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 274 through 276 removed outlier: 4.101A pdb=" N ARG B 339 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 74 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL B 57 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP B 59 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG B 70 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 274 through 276 removed outlier: 4.101A pdb=" N ARG B 339 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 17 through 23 removed outlier: 5.909A pdb=" N GLU C 20 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 10 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.562A pdb=" N GLU C 65 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AC3, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.331A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 165 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 242 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 129 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 273 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.621A pdb=" N LEU D 364 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR D 393 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR D 315 " --> pdb=" O PHE D 462 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.577A pdb=" N THR E 83 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.886A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 212 through 213 removed outlier: 4.153A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AC9, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AD1, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AD2, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AD3, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.254A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 130 through 135 removed outlier: 4.749A pdb=" N GLU H 141 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL H 93 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE H 177 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AD6, first strand: chain 'K' and resid 198 through 205 removed outlier: 5.709A pdb=" N SER K 198 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR K 59 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET K 200 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU K 57 " --> pdb=" O MET K 200 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS K 202 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU K 55 " --> pdb=" O LYS K 202 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY K 204 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA K 237 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN K 253 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE K 239 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AD8, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.789A pdb=" N ALA K 87 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG K 113 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.220A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AE2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AE3, first strand: chain 'M' and resid 49 through 52 removed outlier: 6.739A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.480A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.039A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE7, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.550A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE9, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.164A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.580A pdb=" N THR Q 81 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.164A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 87 through 95 removed outlier: 3.921A pdb=" N LYS S 124 " --> pdb=" O TRP S 77 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 24 through 25 Processing sheet with id=AF5, first strand: chain 'V' and resid 120 through 121 removed outlier: 6.911A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF7, first strand: chain 'Y' and resid 93 through 98 removed outlier: 6.860A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE Y 69 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL Y 84 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLY Y 67 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AF9, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.741A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA f 81 " --> pdb=" O HIS f 76 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG f 74 " --> pdb=" O ARG f 83 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG f 85 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE f 72 " --> pdb=" O ARG f 85 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG2, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AG3, first strand: chain 'n' and resid 177 through 182 removed outlier: 6.678A pdb=" N GLN n 190 " --> pdb=" O ARG n 178 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA n 180 " --> pdb=" O TYR n 188 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR n 188 " --> pdb=" O ALA n 180 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU n 182 " --> pdb=" O GLY n 186 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY n 186 " --> pdb=" O LEU n 182 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'n' and resid 248 through 249 Processing sheet with id=AG5, first strand: chain 'n' and resid 379 through 382 removed outlier: 6.730A pdb=" N PHE n 358 " --> pdb=" O GLY n 381 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR n 357 " --> pdb=" O HIS n 401 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE n 403 " --> pdb=" O THR n 357 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE n 359 " --> pdb=" O ILE n 403 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N HIS n 402 " --> pdb=" O ILE n 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'o' and resid 134 through 138 removed outlier: 8.045A pdb=" N ARG o 135 " --> pdb=" O TYR o 148 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR o 148 " --> pdb=" O ARG o 135 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER o 137 " --> pdb=" O LYS o 146 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL o 106 " --> pdb=" O ILE o 181 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 't' and resid 211 through 212 removed outlier: 4.102A pdb=" N ASN t 119 " --> pdb=" O ARG t 94 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL t 140 " --> pdb=" O GLY t 235 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N CYS t 237 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR t 142 " --> pdb=" O CYS t 237 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 't' and resid 159 through 162 Processing sheet with id=AG9, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.690A pdb=" N HIS u 4 " --> pdb=" O VAL u 13 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AH2, first strand: chain 'x' and resid 122 through 125 removed outlier: 4.492A pdb=" N THR x 100 " --> pdb=" O ARG x 125 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU x 97 " --> pdb=" O LEU x 149 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU x 151 " --> pdb=" O LEU x 97 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR x 99 " --> pdb=" O LEU x 151 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU x 153 " --> pdb=" O THR x 99 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN x 159 " --> pdb=" O LEU x 176 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR x 175 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU x 274 " --> pdb=" O THR x 175 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER x 177 " --> pdb=" O MET x 272 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N MET x 272 " --> pdb=" O SER x 177 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU x 179 " --> pdb=" O PHE x 270 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE x 270 " --> pdb=" O LEU x 179 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU x 197 " --> pdb=" O VAL x 231 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE x 233 " --> pdb=" O GLU x 197 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE x 199 " --> pdb=" O ILE x 233 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS x 235 " --> pdb=" O ILE x 199 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN x 201 " --> pdb=" O CYS x 235 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'x' and resid 122 through 125 removed outlier: 4.492A pdb=" N THR x 100 " --> pdb=" O ARG x 125 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU x 97 " --> pdb=" O LEU x 149 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU x 151 " --> pdb=" O LEU x 97 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR x 99 " --> pdb=" O LEU x 151 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU x 153 " --> pdb=" O THR x 99 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN x 159 " --> pdb=" O LEU x 176 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR x 175 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU x 274 " --> pdb=" O THR x 175 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER x 177 " --> pdb=" O MET x 272 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N MET x 272 " --> pdb=" O SER x 177 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU x 179 " --> pdb=" O PHE x 270 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE x 270 " --> pdb=" O LEU x 179 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG x 275 " --> pdb=" O GLU x 292 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU x 292 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL x 277 " --> pdb=" O PHE x 290 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU x 288 " --> pdb=" O LYS x 279 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'x' and resid 249 through 251 Processing sheet with id=AH5, first strand: chain 'y' and resid 3 through 4 removed outlier: 5.562A pdb=" N LEU y 3 " --> pdb=" O ALA y 206 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'y' and resid 64 through 66 removed outlier: 7.152A pdb=" N VAL y 97 " --> pdb=" O LEU y 70 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL y 72 " --> pdb=" O VAL y 97 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'y' and resid 109 through 110 2303 hydrogen bonds defined for protein. 6549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1207 hydrogen bonds 1958 hydrogen bond angles 0 basepair planarities 507 basepair parallelities 950 stacking parallelities Total time for adding SS restraints: 74.16 Time building geometry restraints manager: 34.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11968 1.32 - 1.45: 32358 1.45 - 1.57: 41921 1.57 - 1.70: 3321 1.70 - 1.82: 202 Bond restraints: 89770 Sorted by residual: bond pdb=" C1' U 1 500 " pdb=" N1 U 1 500 " ideal model delta sigma weight residual 1.470 1.549 -0.079 1.50e-02 4.44e+03 2.79e+01 bond pdb=" C VAL 3 11 " pdb=" O VAL 3 11 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.22e-02 6.72e+03 7.54e+00 bond pdb=" CA VAL 3 11 " pdb=" C VAL 3 11 " ideal model delta sigma weight residual 1.524 1.501 0.022 1.33e-02 5.65e+03 2.83e+00 bond pdb=" CB ARG 4 28 " pdb=" CG ARG 4 28 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" O5' G 2 111 " pdb=" C5' G 2 111 " ideal model delta sigma weight residual 1.420 1.443 -0.023 1.50e-02 4.44e+03 2.40e+00 ... (remaining 89765 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.23: 8237 105.23 - 112.47: 50302 112.47 - 119.70: 29627 119.70 - 126.93: 36732 126.93 - 134.16: 4614 Bond angle restraints: 129512 Sorted by residual: angle pdb=" CA ARG 4 28 " pdb=" CB ARG 4 28 " pdb=" CG ARG 4 28 " ideal model delta sigma weight residual 114.10 123.53 -9.43 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA GLU E 137 " pdb=" CB GLU E 137 " pdb=" CG GLU E 137 " ideal model delta sigma weight residual 114.10 122.98 -8.88 2.00e+00 2.50e-01 1.97e+01 angle pdb=" C ASN J 161 " pdb=" CA ASN J 161 " pdb=" CB ASN J 161 " ideal model delta sigma weight residual 115.79 110.53 5.26 1.19e+00 7.06e-01 1.95e+01 angle pdb=" C GLU y 8 " pdb=" CA GLU y 8 " pdb=" CB GLU y 8 " ideal model delta sigma weight residual 116.34 110.31 6.03 1.40e+00 5.10e-01 1.85e+01 angle pdb=" N ILE m 102 " pdb=" CA ILE m 102 " pdb=" C ILE m 102 " ideal model delta sigma weight residual 113.20 109.12 4.08 9.60e-01 1.09e+00 1.81e+01 ... (remaining 129507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 48233 35.46 - 70.92: 2043 70.92 - 106.38: 181 106.38 - 141.84: 10 141.84 - 177.30: 20 Dihedral angle restraints: 50487 sinusoidal: 31296 harmonic: 19191 Sorted by residual: dihedral pdb=" O4' U 1 258 " pdb=" C1' U 1 258 " pdb=" N1 U 1 258 " pdb=" C2 U 1 258 " ideal model delta sinusoidal sigma weight residual 200.00 41.71 158.29 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U 13314 " pdb=" C1' U 13314 " pdb=" N1 U 13314 " pdb=" C2 U 13314 " ideal model delta sinusoidal sigma weight residual 200.00 44.88 155.12 1 1.50e+01 4.44e-03 8.14e+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 60.44 139.56 1 1.50e+01 4.44e-03 7.51e+01 ... (remaining 50484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 13769 0.046 - 0.091: 1737 0.091 - 0.137: 476 0.137 - 0.182: 39 0.182 - 0.228: 7 Chirality restraints: 16028 Sorted by residual: chirality pdb=" C3' A 1 461 " pdb=" C4' A 1 461 " pdb=" O3' A 1 461 " pdb=" C2' A 1 461 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C2' G 13181 " pdb=" C3' G 13181 " pdb=" O2' G 13181 " pdb=" C1' G 13181 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' U 11154 " pdb=" C4' U 11154 " pdb=" O3' U 11154 " pdb=" C2' U 11154 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 16025 not shown) Planarity restraints: 10396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 150 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO K 151 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO K 151 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 151 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 7 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO P 8 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO P 8 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO P 8 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 193 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C ILE A 193 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE A 193 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 194 " -0.014 2.00e-02 2.50e+03 ... (remaining 10393 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 7951 2.74 - 3.28: 81061 3.28 - 3.82: 167968 3.82 - 4.36: 207044 4.36 - 4.90: 296927 Nonbonded interactions: 760951 Sorted by model distance: nonbonded pdb=" N GLN h 21 " pdb=" OE1 GLN h 21 " model vdw 2.194 2.520 nonbonded pdb=" N GLU 4 37 " pdb=" OE1 GLU 4 37 " model vdw 2.197 2.520 nonbonded pdb=" O2' C 6 181 " pdb=" OP2 A 6 183 " model vdw 2.197 2.440 nonbonded pdb=" O2 U 6 62 " pdb=" N6 A 6 81 " model vdw 2.197 2.520 nonbonded pdb=" OP2 U 1 712 " pdb=" NH2 ARG L 36 " model vdw 2.199 2.520 ... (remaining 760946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1677 5.49 5 S 124 5.16 5 C 46839 2.51 5 N 15649 2.21 5 O 20456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 11.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 30.980 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.550 Process input model: 248.230 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 307.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.003 0.079 89770 Z= 0.212 Angle : 0.476 12.167 129512 Z= 0.253 Chirality : 0.034 0.228 16028 Planarity : 0.003 0.072 10396 Dihedral : 16.624 177.297 38003 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.09 (0.10), residues: 6478 helix: 0.67 (0.10), residues: 2558 sheet: 0.27 (0.18), residues: 879 loop : -0.43 (0.11), residues: 3041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 403 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 84 residues processed: 498 average time/residue: 1.5150 time to fit residues: 1028.5416 Evaluate side-chains 469 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 385 time to evaluate : 5.356 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 80 residues processed: 4 average time/residue: 0.6420 time to fit residues: 11.1196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 684 optimal weight: 50.0000 chunk 614 optimal weight: 3.9990 chunk 341 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 414 optimal weight: 6.9990 chunk 328 optimal weight: 0.0060 chunk 635 optimal weight: 20.0000 chunk 245 optimal weight: 0.0050 chunk 386 optimal weight: 8.9990 chunk 473 optimal weight: 0.0070 chunk 736 optimal weight: 9.9990 overall best weight: 1.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 39 ASN 3 95 GLN 3 180 ASN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 HIS G 95 ASN G 107 GLN G 182 ASN O 51 ASN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN h 25 GLN m 208 ASN m 252 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 GLN v 172 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 89770 Z= 0.180 Angle : 0.539 9.784 129512 Z= 0.276 Chirality : 0.036 0.312 16028 Planarity : 0.004 0.071 10396 Dihedral : 15.303 177.776 27194 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer Outliers : 4.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.46 (0.11), residues: 6478 helix: 1.23 (0.10), residues: 2610 sheet: 0.22 (0.18), residues: 880 loop : -0.44 (0.12), residues: 2988 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 409 time to evaluate : 5.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 214 outliers final: 111 residues processed: 570 average time/residue: 1.5111 time to fit residues: 1184.8251 Evaluate side-chains 496 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 385 time to evaluate : 5.313 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 94 residues processed: 17 average time/residue: 1.0105 time to fit residues: 33.1086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 409 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 612 optimal weight: 0.9980 chunk 501 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 737 optimal weight: 9.9990 chunk 797 optimal weight: 10.0000 chunk 657 optimal weight: 10.0000 chunk 731 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 chunk 591 optimal weight: 40.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 39 ASN 3 95 GLN ** 3 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN C 316 GLN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 ASN O 51 ASN O 102 HIS P 97 ASN ** Q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 HIS S 48 ASN S 61 ASN ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 208 ASN m 252 GLN o 127 GLN v 38 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.180 89770 Z= 0.800 Angle : 0.881 10.393 129512 Z= 0.437 Chirality : 0.056 0.409 16028 Planarity : 0.007 0.090 10396 Dihedral : 15.959 179.499 27194 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer Outliers : 6.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 6478 helix: 0.71 (0.10), residues: 2613 sheet: -0.15 (0.18), residues: 900 loop : -0.74 (0.11), residues: 2965 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 394 time to evaluate : 5.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 285 outliers final: 159 residues processed: 620 average time/residue: 1.5630 time to fit residues: 1328.0966 Evaluate side-chains 536 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 377 time to evaluate : 5.542 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 128 residues processed: 31 average time/residue: 1.0989 time to fit residues: 57.9040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 728 optimal weight: 50.0000 chunk 554 optimal weight: 3.9990 chunk 382 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 352 optimal weight: 30.0000 chunk 495 optimal weight: 5.9990 chunk 740 optimal weight: 40.0000 chunk 783 optimal weight: 0.9980 chunk 386 optimal weight: 2.9990 chunk 701 optimal weight: 40.0000 chunk 211 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 78 GLN ** 5 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 71 GLN 5 258 HIS 5 316 ASN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN N 15 GLN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 15 ASN m 208 ASN o 139 ASN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 172 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 89770 Z= 0.332 Angle : 0.606 8.719 129512 Z= 0.310 Chirality : 0.041 0.350 16028 Planarity : 0.005 0.073 10396 Dihedral : 15.639 179.510 27194 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.32 % Rotamer Outliers : 5.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.14 (0.10), residues: 6478 helix: 1.06 (0.10), residues: 2619 sheet: -0.05 (0.18), residues: 887 loop : -0.69 (0.11), residues: 2972 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 413 time to evaluate : 5.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 266 outliers final: 156 residues processed: 630 average time/residue: 1.5047 time to fit residues: 1311.1815 Evaluate side-chains 543 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 387 time to evaluate : 5.502 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 137 residues processed: 20 average time/residue: 0.9073 time to fit residues: 36.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 652 optimal weight: 1.9990 chunk 444 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 583 optimal weight: 50.0000 chunk 323 optimal weight: 0.7980 chunk 668 optimal weight: 8.9990 chunk 541 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 400 optimal weight: 0.7980 chunk 703 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN L 110 GLN O 51 ASN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN m 252 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 38 GLN v 168 GLN v 172 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 89770 Z= 0.305 Angle : 0.592 10.771 129512 Z= 0.303 Chirality : 0.040 0.342 16028 Planarity : 0.005 0.073 10396 Dihedral : 15.509 179.403 27194 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % Rotamer Outliers : 5.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.27 (0.11), residues: 6478 helix: 1.24 (0.10), residues: 2614 sheet: -0.08 (0.18), residues: 902 loop : -0.66 (0.11), residues: 2962 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 406 time to evaluate : 5.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 256 outliers final: 177 residues processed: 615 average time/residue: 1.5484 time to fit residues: 1319.8758 Evaluate side-chains 559 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 382 time to evaluate : 5.411 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 154 residues processed: 26 average time/residue: 0.9470 time to fit residues: 46.7116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 263 optimal weight: 0.7980 chunk 705 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 460 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 784 optimal weight: 2.9990 chunk 651 optimal weight: 4.9990 chunk 363 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 411 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 15 ASN h 25 GLN o 139 ASN v 33 ASN v 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 89770 Z= 0.183 Angle : 0.545 10.214 129512 Z= 0.280 Chirality : 0.037 0.332 16028 Planarity : 0.004 0.091 10396 Dihedral : 15.433 179.002 27194 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.48 (0.11), residues: 6478 helix: 1.46 (0.10), residues: 2601 sheet: 0.04 (0.18), residues: 891 loop : -0.57 (0.12), residues: 2986 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 395 time to evaluate : 5.480 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 225 outliers final: 165 residues processed: 586 average time/residue: 1.4947 time to fit residues: 1211.1646 Evaluate side-chains 544 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 379 time to evaluate : 5.329 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 151 residues processed: 15 average time/residue: 0.9007 time to fit residues: 28.4134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 756 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 447 optimal weight: 20.0000 chunk 573 optimal weight: 0.0020 chunk 443 optimal weight: 50.0000 chunk 660 optimal weight: 9.9990 chunk 438 optimal weight: 10.0000 chunk 781 optimal weight: 4.9990 chunk 489 optimal weight: 0.0870 chunk 476 optimal weight: 0.9980 chunk 360 optimal weight: 8.9990 overall best weight: 1.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 15 ASN m 252 GLN o 139 ASN o 177 GLN v 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 89770 Z= 0.215 Angle : 0.541 9.828 129512 Z= 0.278 Chirality : 0.037 0.315 16028 Planarity : 0.004 0.072 10396 Dihedral : 15.300 178.898 27194 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer Outliers : 4.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.57 (0.11), residues: 6478 helix: 1.55 (0.10), residues: 2617 sheet: 0.02 (0.18), residues: 898 loop : -0.53 (0.12), residues: 2963 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 397 time to evaluate : 5.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 169 residues processed: 580 average time/residue: 1.5149 time to fit residues: 1223.4911 Evaluate side-chains 549 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 380 time to evaluate : 5.268 Switching outliers to nearest non-outliers outliers start: 169 outliers final: 155 residues processed: 17 average time/residue: 0.9681 time to fit residues: 32.7356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 483 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 466 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 496 optimal weight: 6.9990 chunk 532 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 614 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 95 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 15 ASN o 139 ASN o 177 GLN v 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 89770 Z= 0.334 Angle : 0.597 10.160 129512 Z= 0.305 Chirality : 0.040 0.315 16028 Planarity : 0.005 0.074 10396 Dihedral : 15.351 179.528 27194 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % 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: 0.46 (0.11), residues: 6478 helix: 1.44 (0.10), residues: 2621 sheet: 0.01 (0.18), residues: 891 loop : -0.60 (0.11), residues: 2966 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 397 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 167 residues processed: 581 average time/residue: 1.5144 time to fit residues: 1216.3674 Evaluate side-chains 551 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 384 time to evaluate : 5.334 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 157 residues processed: 12 average time/residue: 0.8275 time to fit residues: 23.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 711 optimal weight: 6.9990 chunk 748 optimal weight: 1.9990 chunk 683 optimal weight: 10.0000 chunk 728 optimal weight: 50.0000 chunk 438 optimal weight: 40.0000 chunk 317 optimal weight: 0.6980 chunk 571 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 658 optimal weight: 1.9990 chunk 688 optimal weight: 20.0000 chunk 725 optimal weight: 40.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 95 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 ASN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 13 GLN h 15 ASN m 252 GLN o 177 GLN ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 38 GLN v 172 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.121 89770 Z= 0.471 Angle : 0.681 11.536 129512 Z= 0.346 Chirality : 0.045 0.325 16028 Planarity : 0.005 0.075 10396 Dihedral : 15.511 179.523 27194 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Rotamer Outliers : 4.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 6478 helix: 1.23 (0.10), residues: 2621 sheet: -0.11 (0.18), residues: 894 loop : -0.66 (0.11), residues: 2963 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 394 time to evaluate : 5.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 171 residues processed: 573 average time/residue: 1.5445 time to fit residues: 1219.9028 Evaluate side-chains 553 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 382 time to evaluate : 5.371 Switching outliers to nearest non-outliers outliers start: 171 outliers final: 156 residues processed: 18 average time/residue: 0.9620 time to fit residues: 34.2892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 478 optimal weight: 4.9990 chunk 770 optimal weight: 0.0010 chunk 470 optimal weight: 2.9990 chunk 365 optimal weight: 7.9990 chunk 535 optimal weight: 6.9990 chunk 807 optimal weight: 40.0000 chunk 743 optimal weight: 50.0000 chunk 643 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 496 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 95 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 ASN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 15 ASN h 25 GLN m 252 GLN ** o 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 168 GLN v 172 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 89770 Z= 0.239 Angle : 0.562 10.500 129512 Z= 0.288 Chirality : 0.038 0.308 16028 Planarity : 0.004 0.072 10396 Dihedral : 15.300 179.449 27194 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 6478 helix: 1.46 (0.10), residues: 2618 sheet: -0.02 (0.18), residues: 896 loop : -0.59 (0.12), residues: 2964 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12956 Ramachandran restraints generated. 6478 Oldfield, 0 Emsley, 6478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 396 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 155 residues processed: 557 average time/residue: 1.5187 time to fit residues: 1173.2735 Evaluate side-chains 542 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 387 time to evaluate : 5.298 Switching outliers to nearest non-outliers outliers start: 155 outliers final: 153 residues processed: 3 average time/residue: 1.0237 time to fit residues: 11.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 511 optimal weight: 0.7980 chunk 685 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 593 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 644 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 661 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 50.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 95 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 HIS S 48 ASN h 15 ASN ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 177 GLN ** o 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.162530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.147831 restraints weight = 137384.590| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 0.87 r_work: 0.3851 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4303 r_free = 0.4303 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4303 r_free = 0.4303 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 89770 Z= 0.256 Angle : 0.567 12.207 129512 Z= 0.291 Chirality : 0.038 0.298 16028 Planarity : 0.004 0.072 10396 Dihedral : 15.205 178.766 27194 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 6478 helix: 1.53 (0.10), residues: 2617 sheet: -0.01 (0.18), residues: 900 loop : -0.57 (0.12), residues: 2961 =============================================================================== Job complete usr+sys time: 19368.50 seconds wall clock time: 342 minutes 5.56 seconds (20525.56 seconds total)