Starting phenix.real_space_refine on Wed Mar 20 18:08:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v93_8645/03_2024/5v93_8645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v93_8645/03_2024/5v93_8645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v93_8645/03_2024/5v93_8645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v93_8645/03_2024/5v93_8645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v93_8645/03_2024/5v93_8645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v93_8645/03_2024/5v93_8645_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4752 5.49 5 S 91 5.16 5 C 71344 2.51 5 N 26973 2.21 5 O 40420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 24": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143580 Number of models: 1 Model: "" Number of chains: 52 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 421 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 358 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 345 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "A" Number of atoms: 66956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 292, 'rna2p_pyr': 164, 'rna3p_pur': 1491, 'rna3p_pyr': 1171} Link IDs: {'rna2p': 456, 'rna3p': 2661} Chain breaks: 1 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1335 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1060 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 476 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 541 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32610 Classifications: {'RNA': 1519} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 79, 'rna3p_pur': 741, 'rna3p_pyr': 586} Link IDs: {'rna2p': 192, 'rna3p': 1326} Chain: "b" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1658 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "e" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1149 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 999 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "i" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "m" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "n" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "q" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 763 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "r" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "s" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "t" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 631 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'TRANS': 81} Chain: "x" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 271 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Time building chain proxies: 54.17, per 1000 atoms: 0.38 Number of scatterers: 143580 At special positions: 0 Unit cell: (237.5, 267.5, 246.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 91 16.00 P 4752 15.00 O 40420 8.00 N 26973 7.00 C 71344 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 66.55 Conformation dependent library (CDL) restraints added in 6.6 seconds 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9706 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 154 helices and 68 sheets defined 35.8% alpha, 17.8% beta 1155 base pairs and 2239 stacking pairs defined. Time for finding SS restraints: 67.57 Creating SS restraints... Processing helix chain '0' and resid 9 through 20 removed outlier: 4.279A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 4.526A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 19 Processing helix chain '2' and resid 20 through 28 removed outlier: 4.018A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 37 through 45 Processing helix chain '3' and resid 51 through 63 removed outlier: 4.969A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) Processing helix chain '6' and resid 38 through 43 removed outlier: 3.724A pdb=" N HIS 6 42 " --> pdb=" O CYS 6 38 " (cutoff:3.500A) Proline residue: 6 43 - end of helix No H-bonds generated for 'chain '6' and resid 38 through 43' Processing helix chain 'C' and resid 30 through 35 removed outlier: 5.840A pdb=" N ARG C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.639A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 200 through 205 removed outlier: 5.485A pdb=" N ASN C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.327A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.997A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 5.445A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 5.908A pdb=" N ASN D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 74 Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.543A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 4.090A pdb=" N PHE E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.585A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLN E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 169 through 176 removed outlier: 5.552A pdb=" N LYS E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 4.238A pdb=" N VAL E 194 " --> pdb=" O ASN E 190 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'F' and resid 13 through 27 removed outlier: 4.622A pdb=" N SER F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 68 removed outlier: 4.001A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.709A pdb=" N ARG F 52 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 8 removed outlier: 4.562A pdb=" N GLN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix No H-bonds generated for 'chain 'G' and resid 3 through 8' Processing helix chain 'G' and resid 59 through 82 removed outlier: 5.923A pdb=" N ARG G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.566A pdb=" N GLN G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 34 removed outlier: 6.552A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 65 through 72 removed outlier: 3.914A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.098A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 removed outlier: 4.487A pdb=" N ILE K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.341A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 78 through 86 Processing helix chain 'L' and resid 93 through 101 Processing helix chain 'L' and resid 129 through 140 Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 110 through 126 Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 Proline residue: N 46 - end of helix Processing helix chain 'N' and resid 59 through 70 removed outlier: 4.006A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 4.493A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 4.733A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 25 removed outlier: 4.150A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER O 25 " --> pdb=" O ARG O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 4.536A pdb=" N ARG O 66 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.848A pdb=" N VAL O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 4.678A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 12 removed outlier: 5.229A pdb=" N PHE P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) Proline residue: P 10 - end of helix Processing helix chain 'Q' and resid 6 through 22 removed outlier: 4.008A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Q 20 " --> pdb=" O SER Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.190A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 73 removed outlier: 3.942A pdb=" N GLU Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN Q 38 " --> pdb=" O LYS Q 34 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Proline residue: Q 118 - end of helix Processing helix chain 'R' and resid 52 through 60 removed outlier: 4.119A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 4.598A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 Processing helix chain 'S' and resid 54 through 70 Processing helix chain 'T' and resid 7 through 12 removed outlier: 4.428A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 7 through 12' Processing helix chain 'T' and resid 17 through 25 removed outlier: 3.692A pdb=" N LEU T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 51 Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.344A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 Processing helix chain 'V' and resid 49 through 57 removed outlier: 5.088A pdb=" N ALA V 53 " --> pdb=" O GLY V 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA V 54 " --> pdb=" O HIS V 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.752A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 39 removed outlier: 3.759A pdb=" N PHE Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 66 removed outlier: 4.785A pdb=" N LEU Y 47 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 42 through 51 removed outlier: 4.122A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.257A pdb=" N PHE c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 47 removed outlier: 4.401A pdb=" N GLU c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU c 47 " --> pdb=" O SER c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.767A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.877A pdb=" N ASP c 89 " --> pdb=" O ARG c 85 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU c 90 " --> pdb=" O ILE c 86 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU c 93 " --> pdb=" O ASP c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.264A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.717A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.708A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 61 Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.717A pdb=" N ARG d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 3.807A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 105 through 116 Processing helix chain 'd' and resid 150 through 157 Processing helix chain 'd' and resid 182 through 187 removed outlier: 3.868A pdb=" N ILE d 186 " --> pdb=" O GLU d 182 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 182 through 187' Processing helix chain 'd' and resid 191 through 201 removed outlier: 5.519A pdb=" N ILE d 195 " --> pdb=" O THR d 191 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 3.936A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 6.273A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 5.484A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 188 removed outlier: 3.659A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG e 187 " --> pdb=" O GLU e 183 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 19 removed outlier: 3.563A pdb=" N ASP f 15 " --> pdb=" O ASP f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 34 removed outlier: 5.173A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 4.734A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.201A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 146 removed outlier: 4.566A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.698A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU h 14 " --> pdb=" O PHE h 10 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 96 through 101 removed outlier: 6.147A pdb=" N GLY h 100 " --> pdb=" O ARG h 96 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU h 101 " --> pdb=" O VAL h 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 96 through 101' Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 71 removed outlier: 4.129A pdb=" N GLN i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 80 removed outlier: 4.706A pdb=" N GLU i 80 " --> pdb=" O VAL i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 112 removed outlier: 4.677A pdb=" N GLY i 98 " --> pdb=" O SER i 94 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA i 99 " --> pdb=" O GLY i 95 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU i 100 " --> pdb=" O GLN i 96 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY i 103 " --> pdb=" O ALA i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 123 Proline residue: i 117 - end of helix Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.702A pdb=" N LYS j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 4.567A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 64 through 69 removed outlier: 4.387A pdb=" N SER k 68 " --> pdb=" O GLY k 64 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR k 69 " --> pdb=" O SER k 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 64 through 69' Processing helix chain 'k' and resid 70 through 88 removed outlier: 3.715A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.068A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Processing helix chain 'l' and resid 22 through 27 removed outlier: 5.430A pdb=" N GLY l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.046A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.815A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.027A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 Processing helix chain 'm' and resid 68 through 85 Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'n' and resid 3 through 12 removed outlier: 5.732A pdb=" N VAL n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 21 removed outlier: 3.503A pdb=" N ALA n 20 " --> pdb=" O PHE n 16 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR n 21 " --> pdb=" O ALA n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 21' Processing helix chain 'n' and resid 40 through 51 removed outlier: 6.102A pdb=" N LEU n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 15 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.864A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 63 removed outlier: 6.060A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 85 Processing helix chain 'r' and resid 34 through 43 removed outlier: 3.862A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.951A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.045A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 68 removed outlier: 3.879A pdb=" N VAL s 67 " --> pdb=" O THR s 63 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY s 68 " --> pdb=" O GLU s 64 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 68' Processing helix chain 's' and resid 70 through 76 Proline residue: s 76 - end of helix Processing helix chain 't' and resid 7 through 42 removed outlier: 4.084A pdb=" N ASN t 11 " --> pdb=" O GLN t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 removed outlier: 3.870A pdb=" N ASP t 59 " --> pdb=" O ASN t 55 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS t 60 " --> pdb=" O ARG t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 86 Processing helix chain 'x' and resid 3 through 25 removed outlier: 3.984A pdb=" N LYS x 7 " --> pdb=" O SER x 3 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG x 9 " --> pdb=" O ILE x 5 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS x 10 " --> pdb=" O LYS x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 26 through 31 removed outlier: 4.424A pdb=" N LEU x 31 " --> pdb=" O VAL x 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 26 through 31' Processing sheet with id= 1, first strand: chain '1' and resid 13 through 16 removed outlier: 7.706A pdb=" N ALA 1 50 " --> pdb=" O GLU 1 16 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '3' and resid 22 through 25 removed outlier: 6.322A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '4' and resid 1 through 5 removed outlier: 4.333A pdb=" N LYS 4 2 " --> pdb=" O LYS 4 33 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN 4 34 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 2 through 6 removed outlier: 8.900A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 76 through 80 removed outlier: 6.483A pdb=" N ALA C 77 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 116 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL C 79 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.868A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 140 through 143 removed outlier: 4.629A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 173 through 176 Processing sheet with id= 9, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.076A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 12 through 18 removed outlier: 4.047A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 49 through 54 removed outlier: 3.522A pdb=" N VAL D 50 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 109 through 113 removed outlier: 4.531A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 180 through 185 removed outlier: 3.663A pdb=" N ILE E 164 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP E 199 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU E 161 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 72 through 75 removed outlier: 3.860A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE F 161 " --> pdb=" O PHE F 137 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 16 through 19 removed outlier: 4.257A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN G 22 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 46 removed outlier: 4.499A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 83 through 90 removed outlier: 6.023A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 95 through 99 removed outlier: 4.290A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA G 107 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.136A pdb=" N LEU H 35 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 15 through 18 Processing sheet with id= 21, first strand: chain 'J' and resid 74 through 78 removed outlier: 8.377A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 17 through 21 removed outlier: 5.769A pdb=" N LYS K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 9 " --> pdb=" O ASN K 82 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE K 86 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS K 59 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 24, first strand: chain 'L' and resid 121 through 124 removed outlier: 4.319A pdb=" N SER L 142 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= 26, first strand: chain 'M' and resid 62 through 66 removed outlier: 5.002A pdb=" N LYS M 63 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR M 32 " --> pdb=" O LEU M 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY M 33 " --> pdb=" O ILE M 132 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE M 132 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG M 130 " --> pdb=" O GLN M 35 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.011A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 32 through 37 removed outlier: 4.855A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 37 through 44 Processing sheet with id= 30, first strand: chain 'P' and resid 48 through 52 removed outlier: 5.276A pdb=" N GLY P 52 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 6 through 9 Processing sheet with id= 32, first strand: chain 'R' and resid 21 through 25 removed outlier: 7.316A pdb=" N TYR R 85 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN R 93 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU R 95 " --> pdb=" O LYS R 70 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS R 70 " --> pdb=" O LEU R 95 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 33 through 38 removed outlier: 4.550A pdb=" N GLU R 34 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL R 65 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY R 63 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 12 through 18 removed outlier: 6.897A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 90 through 98 removed outlier: 3.950A pdb=" N THR S 110 " --> pdb=" O PRO S 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 27 through 33 removed outlier: 5.606A pdb=" N ASN T 27 " --> pdb=" O LEU T 86 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS T 67 " --> pdb=" O GLY T 74 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.684A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG U 32 " --> pdb=" O TYR U 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 6 through 10 Processing sheet with id= 39, first strand: chain 'V' and resid 40 through 46 Processing sheet with id= 40, first strand: chain 'V' and resid 82 through 85 removed outlier: 7.167A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 120 through 125 removed outlier: 7.442A pdb=" N VAL V 176 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 127 through 132 removed outlier: 5.460A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL V 144 " --> pdb=" O VAL V 111 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU V 113 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE V 146 " --> pdb=" O GLU V 113 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLN V 115 " --> pdb=" O ILE V 146 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY V 148 " --> pdb=" O GLN V 115 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 45 through 48 removed outlier: 6.031A pdb=" N GLY W 48 " --> pdb=" O ILE W 80 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 50 through 54 removed outlier: 7.827A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY W 54 " --> pdb=" O THR W 58 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.837A pdb=" N THR X 25 " --> pdb=" O SER X 17 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 34 through 39 removed outlier: 4.172A pdb=" N ASP Z 39 " --> pdb=" O SER Z 2 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER Z 2 " --> pdb=" O ASP Z 39 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN Z 3 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.641A pdb=" N VAL c 63 " --> pdb=" O GLN c 97 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 164 through 170 removed outlier: 4.389A pdb=" N VAL c 151 " --> pdb=" O TYR c 168 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'd' and resid 117 through 120 removed outlier: 7.179A pdb=" N HIS d 117 " --> pdb=" O ARG d 141 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 165 through 169 removed outlier: 8.208A pdb=" N TRP d 165 " --> pdb=" O HIS d 178 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL d 169 " --> pdb=" O ARG d 174 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG d 174 " --> pdb=" O VAL d 169 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 42 through 47 removed outlier: 4.195A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 115 through 119 removed outlier: 3.704A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY e 139 " --> pdb=" O ALA e 156 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER e 158 " --> pdb=" O GLY e 139 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 64 through 72 removed outlier: 4.925A pdb=" N ALA e 66 " --> pdb=" O GLY e 82 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 35 through 38 removed outlier: 3.639A pdb=" N LYS f 36 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU f 10 " --> pdb=" O ILE f 59 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA f 67 " --> pdb=" O ARG f 2 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR f 93 " --> pdb=" O PRO f 3 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 40 through 43 removed outlier: 4.634A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 45 through 48 removed outlier: 7.123A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.981A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP h 48 " --> pdb=" O GLN h 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.137A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 26 through 30 removed outlier: 4.469A pdb=" N VAL i 40 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 42 through 52 removed outlier: 4.560A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 74 through 78 removed outlier: 4.845A pdb=" N ASP j 75 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 39 through 46 removed outlier: 4.256A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY k 118 " --> pdb=" O VAL k 92 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL k 94 " --> pdb=" O GLY k 118 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.150A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.111A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 5 through 11 removed outlier: 4.361A pdb=" N GLY p 38 " --> pdb=" O VAL p 20 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 60 through 64 removed outlier: 6.585A pdb=" N SER q 113 " --> pdb=" O VAL q 129 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 72 through 84 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 's' and resid 48 through 53 removed outlier: 5.361A pdb=" N LYS s 56 " --> pdb=" O ASP s 53 " (cutoff:3.500A) 1579 hydrogen bonds defined for protein. 4665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2977 hydrogen bonds 5004 hydrogen bond angles 0 basepair planarities 1155 basepair parallelities 2239 stacking parallelities Total time for adding SS restraints: 209.93 Time building geometry restraints manager: 70.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 11527 1.29 - 1.42: 71439 1.42 - 1.56: 63758 1.56 - 1.69: 9519 1.69 - 1.82: 152 Bond restraints: 156395 Sorted by residual: bond pdb=" C UAL b 3 " pdb=" N MYN b 4 " ideal model delta sigma weight residual 1.329 1.494 -0.165 1.40e-02 5.10e+03 1.39e+02 bond pdb=" CB MYN b 4 " pdb=" CG MYN b 4 " ideal model delta sigma weight residual 1.526 1.310 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C DPP b 5 " pdb=" N ALA b 6 " ideal model delta sigma weight residual 1.329 1.477 -0.148 1.40e-02 5.10e+03 1.12e+02 bond pdb=" C DPP b 2 " pdb=" N UAL b 3 " ideal model delta sigma weight residual 1.329 1.464 -0.135 1.40e-02 5.10e+03 9.34e+01 bond pdb=" CB MYN b 4 " pdb=" N1 MYN b 4 " ideal model delta sigma weight residual 1.450 1.620 -0.170 2.00e-02 2.50e+03 7.23e+01 ... (remaining 156390 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.89: 26357 105.89 - 113.87: 98019 113.87 - 121.85: 73721 121.85 - 129.83: 33519 129.83 - 137.81: 3292 Bond angle restraints: 234908 Sorted by residual: angle pdb=" N VAL e 105 " pdb=" CA VAL e 105 " pdb=" C VAL e 105 " ideal model delta sigma weight residual 108.63 115.30 -6.67 8.60e-01 1.35e+00 6.01e+01 angle pdb=" C UAL b 3 " pdb=" CA UAL b 3 " pdb=" CB UAL b 3 " ideal model delta sigma weight residual 110.50 122.00 -11.50 1.50e+00 4.44e-01 5.88e+01 angle pdb=" C UAL b 3 " pdb=" N MYN b 4 " pdb=" CA MYN b 4 " ideal model delta sigma weight residual 121.70 111.46 10.24 1.80e+00 3.09e-01 3.24e+01 angle pdb=" C TYR d 31 " pdb=" N PRO d 32 " pdb=" CD PRO d 32 " ideal model delta sigma weight residual 125.00 101.91 23.09 4.10e+00 5.95e-02 3.17e+01 angle pdb=" N UAL b 3 " pdb=" CA UAL b 3 " pdb=" CB UAL b 3 " ideal model delta sigma weight residual 110.40 118.76 -8.36 1.50e+00 4.44e-01 3.11e+01 ... (remaining 234903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 89299 35.65 - 71.31: 10364 71.31 - 106.96: 1194 106.96 - 142.62: 4 142.62 - 178.27: 12 Dihedral angle restraints: 100873 sinusoidal: 85768 harmonic: 15105 Sorted by residual: dihedral pdb=" N KBE b 1 " pdb=" C KBE b 1 " pdb=" CA KBE b 1 " pdb=" CB KBE b 1 " ideal model delta harmonic sigma weight residual 122.80 26.06 96.74 0 2.50e+00 1.60e-01 1.50e+03 dihedral pdb=" C KBE b 1 " pdb=" N KBE b 1 " pdb=" CA KBE b 1 " pdb=" CB KBE b 1 " ideal model delta harmonic sigma weight residual -122.60 -46.54 -76.06 0 2.50e+00 1.60e-01 9.26e+02 dihedral pdb=" C UAL b 3 " pdb=" N UAL b 3 " pdb=" CA UAL b 3 " pdb=" CB UAL b 3 " ideal model delta harmonic sigma weight residual -122.60 -179.94 57.34 0 2.50e+00 1.60e-01 5.26e+02 ... (remaining 100870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 28873 0.114 - 0.229: 1197 0.229 - 0.343: 34 0.343 - 0.458: 1 0.458 - 0.572: 1 Chirality restraints: 30106 Sorted by residual: chirality pdb=" CA PRO d 33 " pdb=" N PRO d 33 " pdb=" C PRO d 33 " pdb=" CB PRO d 33 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CB ILE r 64 " pdb=" CA ILE r 64 " pdb=" CG1 ILE r 64 " pdb=" CG2 ILE r 64 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3' C A1814 " pdb=" C4' C A1814 " pdb=" O3' C A1814 " pdb=" C2' C A1814 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 30103 not shown) Planarity restraints: 12132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR d 31 " 0.112 5.00e-02 4.00e+02 1.76e-01 4.96e+01 pdb=" N PRO d 32 " -0.304 5.00e-02 4.00e+02 pdb=" CA PRO d 32 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO d 32 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C a1354 " 0.014 2.00e-02 2.50e+03 3.06e-02 2.10e+01 pdb=" N1 C a1354 " -0.014 2.00e-02 2.50e+03 pdb=" C2 C a1354 " 0.068 2.00e-02 2.50e+03 pdb=" O2 C a1354 " -0.054 2.00e-02 2.50e+03 pdb=" N3 C a1354 " 0.007 2.00e-02 2.50e+03 pdb=" C4 C a1354 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C a1354 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C a1354 " -0.017 2.00e-02 2.50e+03 pdb=" C6 C a1354 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2331 " -0.038 2.00e-02 2.50e+03 2.59e-02 1.84e+01 pdb=" N9 A A2331 " 0.013 2.00e-02 2.50e+03 pdb=" C8 A A2331 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A A2331 " -0.016 2.00e-02 2.50e+03 pdb=" C5 A A2331 " 0.038 2.00e-02 2.50e+03 pdb=" C6 A A2331 " -0.032 2.00e-02 2.50e+03 pdb=" N6 A A2331 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A2331 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A2331 " -0.018 2.00e-02 2.50e+03 pdb=" N3 A A2331 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A2331 " 0.051 2.00e-02 2.50e+03 ... (remaining 12129 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 1407 2.54 - 3.13: 113292 3.13 - 3.72: 288276 3.72 - 4.31: 380294 4.31 - 4.90: 514968 Nonbonded interactions: 1298237 Sorted by model distance: nonbonded pdb=" O GLY i 45 " pdb=" OG SER i 81 " model vdw 1.951 2.440 nonbonded pdb=" OG1 THR G 78 " pdb=" OH TYR G 84 " model vdw 1.955 2.440 nonbonded pdb=" O2' U a 913 " pdb=" O2' G a1072 " model vdw 1.967 2.440 nonbonded pdb=" O2' C a 708 " pdb=" O4' G a 725 " model vdw 1.974 2.440 nonbonded pdb=" O2' G A1492 " pdb=" O2' G A2453 " model vdw 1.979 2.440 ... (remaining 1298232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.120 Extract box with map and model: 12.030 Check model and map are aligned: 1.530 Set scattering table: 0.980 Process input model: 496.260 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 517.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.010 0.216 156395 Z= 0.607 Angle : 1.088 23.095 234908 Z= 0.556 Chirality : 0.054 0.572 30106 Planarity : 0.009 0.176 12132 Dihedral : 21.996 178.272 91167 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.11 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -2.37 (0.11), residues: 5224 helix: -0.77 (0.11), residues: 1582 sheet: -1.47 (0.17), residues: 909 loop : -2.11 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP k 54 HIS 0.035 0.005 HIS C 53 PHE 0.035 0.004 PHE 2 8 TYR 0.046 0.004 TYR C 84 ARG 0.017 0.002 ARG Q 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1694 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1694 time to evaluate : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 27 LEU cc_start: 0.5056 (tp) cc_final: 0.4702 (tp) REVERT: 1 20 HIS cc_start: 0.6272 (m170) cc_final: 0.5903 (m170) REVERT: 1 35 ARG cc_start: 0.7061 (mtm180) cc_final: 0.6585 (ptp-110) REVERT: 3 22 ILE cc_start: 0.8987 (mt) cc_final: 0.8715 (mm) REVERT: 3 30 ARG cc_start: 0.6423 (mmm160) cc_final: 0.5967 (mtp85) REVERT: C 23 GLU cc_start: 0.7841 (pm20) cc_final: 0.7572 (mp0) REVERT: C 81 HIS cc_start: 0.8517 (m-70) cc_final: 0.7930 (m-70) REVERT: C 192 THR cc_start: 0.8709 (m) cc_final: 0.8063 (p) REVERT: D 51 GLN cc_start: 0.7616 (mt0) cc_final: 0.7385 (mt0) REVERT: D 132 PHE cc_start: 0.8526 (m-10) cc_final: 0.8135 (m-10) REVERT: D 135 GLN cc_start: 0.7996 (mp10) cc_final: 0.7443 (mt0) REVERT: D 162 LYS cc_start: 0.8534 (tttt) cc_final: 0.8314 (tptt) REVERT: D 195 LYS cc_start: 0.8622 (tttt) cc_final: 0.8249 (tttp) REVERT: E 37 ILE cc_start: 0.8203 (pt) cc_final: 0.7431 (tt) REVERT: E 47 GLN cc_start: 0.8023 (mt0) cc_final: 0.7232 (mt0) REVERT: E 59 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8428 (mttm) REVERT: E 123 ASP cc_start: 0.8152 (t70) cc_final: 0.7650 (t0) REVERT: E 127 ASN cc_start: 0.7556 (m-40) cc_final: 0.6887 (m110) REVERT: E 173 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8455 (mmmt) REVERT: E 190 ASN cc_start: 0.7939 (p0) cc_final: 0.7200 (p0) REVERT: F 37 THR cc_start: 0.6371 (t) cc_final: 0.5957 (t) REVERT: F 171 ASP cc_start: 0.7886 (m-30) cc_final: 0.7653 (m-30) REVERT: G 62 ASN cc_start: 0.7265 (m-40) cc_final: 0.6728 (m-40) REVERT: G 76 LEU cc_start: 0.8357 (mt) cc_final: 0.7923 (mt) REVERT: G 78 THR cc_start: 0.8956 (p) cc_final: 0.8732 (p) REVERT: G 115 VAL cc_start: 0.8846 (t) cc_final: 0.8460 (p) REVERT: G 122 ILE cc_start: 0.6654 (tt) cc_final: 0.6123 (mp) REVERT: J 72 LYS cc_start: 0.7559 (tttp) cc_final: 0.7302 (tttt) REVERT: J 73 MET cc_start: 0.7165 (mmm) cc_final: 0.6679 (mmp) REVERT: J 102 GLU cc_start: 0.8371 (tt0) cc_final: 0.8117 (tt0) REVERT: J 123 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7927 (mmt-90) REVERT: J 132 HIS cc_start: 0.4870 (t-170) cc_final: 0.3311 (t70) REVERT: J 136 GLN cc_start: 0.8541 (tp40) cc_final: 0.8332 (tp40) REVERT: K 3 GLN cc_start: 0.7611 (pt0) cc_final: 0.7220 (pt0) REVERT: K 6 SER cc_start: 0.8957 (t) cc_final: 0.8663 (p) REVERT: K 29 SER cc_start: 0.9228 (m) cc_final: 0.9014 (p) REVERT: K 82 ASN cc_start: 0.7986 (m-40) cc_final: 0.7722 (m-40) REVERT: M 110 ASN cc_start: 0.6884 (t0) cc_final: 0.6575 (m-40) REVERT: M 132 ILE cc_start: 0.7691 (mt) cc_final: 0.7122 (tp) REVERT: N 27 SER cc_start: 0.9297 (m) cc_final: 0.8846 (p) REVERT: N 34 ILE cc_start: 0.9210 (mm) cc_final: 0.8690 (mm) REVERT: N 90 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7028 (ttp-170) REVERT: N 107 ASN cc_start: 0.8786 (t0) cc_final: 0.8512 (t0) REVERT: O 34 VAL cc_start: 0.9007 (t) cc_final: 0.8793 (p) REVERT: O 61 ILE cc_start: 0.8126 (pt) cc_final: 0.7248 (pt) REVERT: O 96 VAL cc_start: 0.8645 (t) cc_final: 0.8224 (p) REVERT: O 104 TYR cc_start: 0.7523 (t80) cc_final: 0.7262 (t80) REVERT: P 20 ASN cc_start: 0.8227 (m-40) cc_final: 0.7752 (m110) REVERT: P 23 ASP cc_start: 0.7876 (m-30) cc_final: 0.7674 (m-30) REVERT: P 24 THR cc_start: 0.8858 (m) cc_final: 0.8601 (p) REVERT: P 26 ASN cc_start: 0.7729 (t0) cc_final: 0.7399 (t0) REVERT: P 60 VAL cc_start: 0.9017 (m) cc_final: 0.7705 (p) REVERT: R 5 TYR cc_start: 0.7491 (p90) cc_final: 0.6985 (p90) REVERT: S 16 LYS cc_start: 0.8751 (pttt) cc_final: 0.8428 (pttm) REVERT: T 39 LYS cc_start: 0.8842 (mttt) cc_final: 0.8237 (mtmm) REVERT: T 54 VAL cc_start: 0.9164 (t) cc_final: 0.8702 (m) REVERT: T 84 VAL cc_start: 0.9563 (t) cc_final: 0.9322 (p) REVERT: T 95 LEU cc_start: 0.6758 (mt) cc_final: 0.6412 (pp) REVERT: V 92 HIS cc_start: 0.7806 (t-90) cc_final: 0.7499 (t70) REVERT: W 32 LYS cc_start: 0.9060 (mttt) cc_final: 0.8842 (mttp) REVERT: X 17 SER cc_start: 0.9211 (t) cc_final: 0.8729 (p) REVERT: X 57 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7818 (mmtm) REVERT: Y 32 LEU cc_start: 0.9121 (mt) cc_final: 0.8536 (mt) REVERT: Y 41 LEU cc_start: 0.7029 (tp) cc_final: 0.6413 (tp) REVERT: c 22 TRP cc_start: 0.5516 (p90) cc_final: 0.4675 (p90) REVERT: c 23 TYR cc_start: 0.4702 (t80) cc_final: 0.4384 (t80) REVERT: d 66 GLN cc_start: 0.7487 (tt0) cc_final: 0.7101 (mp10) REVERT: d 85 LEU cc_start: 0.7063 (mt) cc_final: 0.6729 (tt) REVERT: e 95 VAL cc_start: 0.7599 (t) cc_final: 0.7317 (t) REVERT: h 5 ASP cc_start: 0.5955 (t0) cc_final: 0.5644 (t0) REVERT: h 18 ASN cc_start: 0.8216 (m-40) cc_final: 0.7936 (m-40) REVERT: i 116 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7452 (mmp80) REVERT: k 67 LYS cc_start: 0.7937 (pttt) cc_final: 0.7425 (tptt) REVERT: k 103 ARG cc_start: 0.6341 (mtt180) cc_final: 0.5466 (mmp80) REVERT: n 61 TRP cc_start: 0.4259 (m-10) cc_final: 0.4038 (m-10) REVERT: o 21 ASP cc_start: 0.4855 (t0) cc_final: 0.4630 (t0) REVERT: o 24 SER cc_start: 0.7943 (t) cc_final: 0.7178 (m) REVERT: o 38 ASP cc_start: 0.7783 (m-30) cc_final: 0.6883 (m-30) REVERT: o 53 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7230 (ttm170) REVERT: p 9 ARG cc_start: 0.5264 (ttm-80) cc_final: 0.4605 (ttp80) REVERT: p 71 LEU cc_start: 0.7643 (mt) cc_final: 0.7206 (mt) REVERT: t 6 SER cc_start: 0.6036 (m) cc_final: 0.5513 (t) REVERT: t 19 LEU cc_start: 0.8805 (tp) cc_final: 0.8497 (tp) REVERT: t 22 LYS cc_start: 0.8314 (pttt) cc_final: 0.8102 (pttm) REVERT: t 25 LYS cc_start: 0.8711 (mttt) cc_final: 0.8418 (mtpp) REVERT: x 19 LYS cc_start: 0.7359 (tptt) cc_final: 0.7152 (mptt) outliers start: 0 outliers final: 0 residues processed: 1694 average time/residue: 1.4505 time to fit residues: 3978.7794 Evaluate side-chains 1088 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1088 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 831 optimal weight: 7.9990 chunk 746 optimal weight: 20.0000 chunk 414 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 503 optimal weight: 3.9990 chunk 398 optimal weight: 8.9990 chunk 772 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 469 optimal weight: 5.9990 chunk 574 optimal weight: 5.9990 chunk 894 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 31 ASN 6 6 HIS C 96 HIS C 122 ASN C 227 ASN D 51 GLN D 139 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 34 GLN G 75 ASN G 98 GLN G 144 GLN J 47 ASN J 85 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 HIS ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN P 79 ASN Q 11 HIS Q 72 ASN Q 81 GLN S 67 ASN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 ASN T 61 ASN ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 HIS W 46 HIS Y 35 GLN c 138 GLN d 66 GLN d 193 GLN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 179 GLN h 117 GLN i 28 GLN j 64 HIS k 32 HIS ** l 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 8 ASN o 46 HIS r 61 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 22 GLN t 55 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 156395 Z= 0.304 Angle : 0.837 27.055 234908 Z= 0.408 Chirality : 0.039 0.700 30106 Planarity : 0.008 0.132 12132 Dihedral : 23.218 178.646 80755 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.73 % Favored : 90.89 % Rotamer: Outliers : 4.09 % Allowed : 11.78 % Favored : 84.13 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.11), residues: 5224 helix: -0.30 (0.12), residues: 1581 sheet: -1.31 (0.17), residues: 876 loop : -1.96 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP s 34 HIS 0.021 0.002 HIS U 4 PHE 0.044 0.003 PHE E 150 TYR 0.039 0.003 TYR o 15 ARG 0.016 0.001 ARG h 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1232 time to evaluate : 5.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 HIS cc_start: 0.6564 (m170) cc_final: 0.6192 (m170) REVERT: 3 21 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7340 (tttt) REVERT: 3 22 ILE cc_start: 0.9103 (mt) cc_final: 0.8705 (mm) REVERT: 3 30 ARG cc_start: 0.6612 (mmm160) cc_final: 0.6139 (mtp85) REVERT: C 184 ARG cc_start: 0.7744 (mtp-110) cc_final: 0.7417 (mtp-110) REVERT: C 192 THR cc_start: 0.8840 (m) cc_final: 0.8187 (p) REVERT: C 214 TRP cc_start: 0.8790 (m-10) cc_final: 0.7626 (m-10) REVERT: C 263 SER cc_start: 0.9130 (m) cc_final: 0.8920 (t) REVERT: D 51 GLN cc_start: 0.7422 (mt0) cc_final: 0.6420 (mt0) REVERT: D 132 PHE cc_start: 0.8688 (m-10) cc_final: 0.8183 (m-10) REVERT: D 135 GLN cc_start: 0.8155 (mp10) cc_final: 0.7458 (mp10) REVERT: D 162 LYS cc_start: 0.8537 (tttt) cc_final: 0.8329 (tptt) REVERT: E 37 ILE cc_start: 0.8294 (pt) cc_final: 0.7968 (tt) REVERT: E 59 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8317 (mttm) REVERT: E 123 ASP cc_start: 0.8240 (t70) cc_final: 0.7820 (t0) REVERT: E 127 ASN cc_start: 0.7493 (m-40) cc_final: 0.7116 (m-40) REVERT: E 140 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 157 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7533 (mpp80) REVERT: E 173 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8430 (mmmt) REVERT: E 178 LEU cc_start: 0.8853 (mt) cc_final: 0.8472 (mt) REVERT: F 33 MET cc_start: 0.5924 (mmt) cc_final: 0.5159 (mmt) REVERT: F 34 GLN cc_start: 0.7308 (tm130) cc_final: 0.6003 (tm-30) REVERT: F 37 THR cc_start: 0.6185 (t) cc_final: 0.5902 (t) REVERT: G 42 LYS cc_start: 0.7010 (pttm) cc_final: 0.6787 (pttm) REVERT: G 76 LEU cc_start: 0.8112 (mt) cc_final: 0.7841 (mt) REVERT: G 82 GLN cc_start: 0.5952 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: G 158 TYR cc_start: 0.6759 (m-10) cc_final: 0.6469 (m-10) REVERT: H 1 MET cc_start: 0.7031 (tpt) cc_final: 0.6508 (ttm) REVERT: H 23 ASP cc_start: 0.7673 (t0) cc_final: 0.7331 (t0) REVERT: H 27 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7556 (ttp-110) REVERT: J 57 ILE cc_start: 0.8523 (mm) cc_final: 0.8117 (mm) REVERT: J 60 ASP cc_start: 0.8137 (t0) cc_final: 0.7897 (t0) REVERT: J 136 GLN cc_start: 0.8442 (tp40) cc_final: 0.8239 (tp40) REVERT: K 6 SER cc_start: 0.9252 (t) cc_final: 0.8887 (p) REVERT: K 107 ARG cc_start: 0.8299 (mmp80) cc_final: 0.7107 (mmp80) REVERT: K 112 MET cc_start: 0.7930 (tpt) cc_final: 0.7458 (tpp) REVERT: L 58 MET cc_start: 0.8373 (mpp) cc_final: 0.8128 (mpp) REVERT: L 63 LEU cc_start: 0.8993 (tp) cc_final: 0.8783 (tp) REVERT: L 73 GLU cc_start: 0.7435 (tp30) cc_final: 0.7225 (tp30) REVERT: M 110 ASN cc_start: 0.6781 (t0) cc_final: 0.6434 (m-40) REVERT: M 111 GLU cc_start: 0.6534 (mp0) cc_final: 0.6313 (mp0) REVERT: M 132 ILE cc_start: 0.7418 (mt) cc_final: 0.6875 (tt) REVERT: N 27 SER cc_start: 0.9270 (m) cc_final: 0.8822 (p) REVERT: N 30 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7612 (tm-30) REVERT: N 34 ILE cc_start: 0.9341 (mm) cc_final: 0.8931 (mm) REVERT: N 104 LYS cc_start: 0.7932 (ptmm) cc_final: 0.7693 (ptpp) REVERT: N 107 ASN cc_start: 0.8780 (t0) cc_final: 0.8465 (t0) REVERT: O 104 TYR cc_start: 0.7661 (t80) cc_final: 0.7455 (t80) REVERT: P 20 ASN cc_start: 0.7982 (m-40) cc_final: 0.7642 (m110) REVERT: P 24 THR cc_start: 0.8827 (m) cc_final: 0.8579 (p) REVERT: P 26 ASN cc_start: 0.7245 (t0) cc_final: 0.6980 (t0) REVERT: P 72 THR cc_start: 0.8971 (p) cc_final: 0.8735 (p) REVERT: Q 74 ILE cc_start: 0.8965 (tp) cc_final: 0.8667 (pt) REVERT: Q 102 ASP cc_start: 0.8170 (t0) cc_final: 0.7912 (t0) REVERT: R 79 PHE cc_start: 0.8906 (t80) cc_final: 0.8686 (t80) REVERT: S 16 LYS cc_start: 0.8822 (pttt) cc_final: 0.8357 (pttm) REVERT: T 39 LYS cc_start: 0.8736 (mttt) cc_final: 0.8506 (mttm) REVERT: U 2 LYS cc_start: 0.6825 (mmmm) cc_final: 0.6530 (mmmm) REVERT: U 12 ILE cc_start: 0.9213 (pt) cc_final: 0.8598 (tt) REVERT: U 99 LYS cc_start: 0.5531 (ptmt) cc_final: 0.5328 (tmtt) REVERT: V 24 ARG cc_start: 0.8545 (ptp-110) cc_final: 0.8191 (ptp-110) REVERT: V 72 LYS cc_start: 0.6972 (mtmm) cc_final: 0.6260 (mptt) REVERT: V 91 GLN cc_start: 0.7885 (mp10) cc_final: 0.7221 (mp10) REVERT: V 92 HIS cc_start: 0.7738 (t-90) cc_final: 0.7414 (t70) REVERT: W 32 LYS cc_start: 0.8931 (mttt) cc_final: 0.7778 (mttp) REVERT: W 41 ARG cc_start: 0.7776 (ptp90) cc_final: 0.7014 (ptp-170) REVERT: X 17 SER cc_start: 0.9299 (t) cc_final: 0.8784 (p) REVERT: Y 11 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.7499 (mtt-85) REVERT: Y 17 GLU cc_start: 0.8011 (mp0) cc_final: 0.7780 (mp0) REVERT: Y 30 PHE cc_start: 0.8624 (t80) cc_final: 0.8421 (t80) REVERT: Z 13 ILE cc_start: 0.8880 (mm) cc_final: 0.8636 (mm) REVERT: c 22 TRP cc_start: 0.5406 (p90) cc_final: 0.4610 (p90) REVERT: c 23 TYR cc_start: 0.4853 (t80) cc_final: 0.4374 (t80) REVERT: d 17 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6373 (m) REVERT: d 53 LYS cc_start: 0.6365 (ttpt) cc_final: 0.6060 (ttpt) REVERT: e 62 PHE cc_start: 0.7564 (m-80) cc_final: 0.7314 (m-10) REVERT: e 93 LYS cc_start: 0.8725 (mttm) cc_final: 0.8466 (mttt) REVERT: e 182 GLU cc_start: 0.8143 (pm20) cc_final: 0.6748 (pm20) REVERT: h 30 SER cc_start: 0.8101 (p) cc_final: 0.7838 (t) REVERT: h 51 THR cc_start: 0.5871 (OUTLIER) cc_final: 0.5335 (m) REVERT: h 105 ILE cc_start: 0.8030 (mt) cc_final: 0.7712 (mm) REVERT: i 116 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7498 (mmp80) REVERT: k 67 LYS cc_start: 0.7718 (pttt) cc_final: 0.7287 (tptt) REVERT: k 103 ARG cc_start: 0.6264 (mtt180) cc_final: 0.5402 (mmp80) REVERT: l 1 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.5204 (mmt) REVERT: l 66 TYR cc_start: 0.6783 (t80) cc_final: 0.6542 (t80) REVERT: m 90 LEU cc_start: 0.7086 (mt) cc_final: 0.6847 (mp) REVERT: o 7 GLN cc_start: 0.7233 (mp10) cc_final: 0.6906 (mp10) REVERT: p 9 ARG cc_start: 0.5558 (ttm-80) cc_final: 0.4900 (ttp80) REVERT: q 126 TRP cc_start: 0.7300 (m100) cc_final: 0.6802 (m100) REVERT: r 66 LEU cc_start: 0.8706 (mt) cc_final: 0.8335 (pp) REVERT: s 71 LEU cc_start: 0.7255 (mt) cc_final: 0.6822 (mm) REVERT: t 6 SER cc_start: 0.5977 (m) cc_final: 0.5667 (t) REVERT: t 19 LEU cc_start: 0.8967 (tp) cc_final: 0.8493 (tp) REVERT: t 25 LYS cc_start: 0.8830 (mttt) cc_final: 0.8469 (mtpp) outliers start: 178 outliers final: 106 residues processed: 1300 average time/residue: 1.3526 time to fit residues: 2931.9061 Evaluate side-chains 1174 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1063 time to evaluate : 5.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 6 residue 6 HIS Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 107 TYR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 497 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 744 optimal weight: 30.0000 chunk 609 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 896 optimal weight: 20.0000 chunk 968 optimal weight: 8.9990 chunk 798 optimal weight: 50.0000 chunk 888 optimal weight: 40.0000 chunk 305 optimal weight: 10.0000 chunk 718 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS ** 1 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 61 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 156395 Z= 0.304 Angle : 0.837 27.055 234908 Z= 0.408 Chirality : 0.039 0.700 30106 Planarity : 0.008 0.132 12132 Dihedral : 23.218 178.646 80755 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.73 % Favored : 90.89 % Rotamer: Outliers : 2.57 % Allowed : 17.07 % Favored : 80.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.11), residues: 5224 helix: -0.30 (0.12), residues: 1581 sheet: -1.31 (0.17), residues: 876 loop : -1.96 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP s 34 HIS 0.021 0.002 HIS U 4 PHE 0.044 0.003 PHE E 150 TYR 0.039 0.003 TYR o 15 ARG 0.016 0.001 ARG h 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1063 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 HIS cc_start: 0.6405 (m170) cc_final: 0.6192 (m170) REVERT: 3 21 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7341 (tttt) REVERT: 3 22 ILE cc_start: 0.9126 (mt) cc_final: 0.8704 (mm) REVERT: 3 30 ARG cc_start: 0.6586 (mmm160) cc_final: 0.6139 (mtp85) REVERT: C 192 THR cc_start: 0.8834 (m) cc_final: 0.8190 (p) REVERT: C 214 TRP cc_start: 0.8765 (m-10) cc_final: 0.7629 (m-10) REVERT: C 263 SER cc_start: 0.9136 (m) cc_final: 0.8914 (t) REVERT: D 132 PHE cc_start: 0.8688 (m-10) cc_final: 0.8186 (m-10) REVERT: D 135 GLN cc_start: 0.8159 (mp10) cc_final: 0.7455 (mp10) REVERT: D 162 LYS cc_start: 0.8561 (tttt) cc_final: 0.8330 (tptt) REVERT: E 59 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8314 (mttm) REVERT: E 123 ASP cc_start: 0.8241 (t70) cc_final: 0.7821 (t0) REVERT: E 127 ASN cc_start: 0.7514 (m-40) cc_final: 0.7116 (m-40) REVERT: E 140 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 157 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7538 (mpp80) REVERT: E 173 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8428 (mmmt) REVERT: E 178 LEU cc_start: 0.8855 (mt) cc_final: 0.8470 (mt) REVERT: F 37 THR cc_start: 0.6202 (t) cc_final: 0.5908 (t) REVERT: G 78 THR cc_start: 0.9269 (p) cc_final: 0.8894 (p) REVERT: G 82 GLN cc_start: 0.5992 (OUTLIER) cc_final: 0.5745 (mp10) REVERT: G 158 TYR cc_start: 0.6744 (m-10) cc_final: 0.6467 (m-10) REVERT: H 1 MET cc_start: 0.7100 (tpt) cc_final: 0.6508 (ttm) REVERT: H 23 ASP cc_start: 0.7573 (t0) cc_final: 0.7331 (t0) REVERT: H 27 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7558 (ttp-110) REVERT: J 57 ILE cc_start: 0.8531 (mm) cc_final: 0.8110 (mm) REVERT: J 102 GLU cc_start: 0.8239 (tt0) cc_final: 0.8012 (mt-10) REVERT: J 136 GLN cc_start: 0.8446 (tp40) cc_final: 0.8237 (tp40) REVERT: K 6 SER cc_start: 0.9246 (t) cc_final: 0.8882 (p) REVERT: K 107 ARG cc_start: 0.8264 (mmp80) cc_final: 0.7102 (mmp80) REVERT: K 112 MET cc_start: 0.7747 (tpt) cc_final: 0.7453 (tpp) REVERT: L 58 MET cc_start: 0.8372 (mpp) cc_final: 0.8128 (mpp) REVERT: L 63 LEU cc_start: 0.8993 (tp) cc_final: 0.8784 (tp) REVERT: L 73 GLU cc_start: 0.7435 (tp30) cc_final: 0.7223 (tp30) REVERT: M 110 ASN cc_start: 0.6833 (t0) cc_final: 0.6430 (m-40) REVERT: M 111 GLU cc_start: 0.6610 (mp0) cc_final: 0.6312 (mp0) REVERT: M 132 ILE cc_start: 0.7036 (mt) cc_final: 0.6683 (tp) REVERT: N 27 SER cc_start: 0.9249 (m) cc_final: 0.8827 (p) REVERT: N 30 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7617 (tm-30) REVERT: N 34 ILE cc_start: 0.9346 (mm) cc_final: 0.8925 (mm) REVERT: N 103 ARG cc_start: 0.6637 (mtp180) cc_final: 0.6247 (mtp180) REVERT: N 104 LYS cc_start: 0.7919 (ptmm) cc_final: 0.7708 (ptpp) REVERT: N 107 ASN cc_start: 0.8799 (t0) cc_final: 0.8467 (t0) REVERT: P 24 THR cc_start: 0.8857 (m) cc_final: 0.8580 (p) REVERT: P 72 THR cc_start: 0.8997 (p) cc_final: 0.8740 (p) REVERT: Q 74 ILE cc_start: 0.8926 (tp) cc_final: 0.8662 (pt) REVERT: Q 102 ASP cc_start: 0.8123 (t0) cc_final: 0.7908 (t0) REVERT: S 16 LYS cc_start: 0.8819 (pttt) cc_final: 0.8356 (pttm) REVERT: T 39 LYS cc_start: 0.8718 (mttt) cc_final: 0.8481 (mttm) REVERT: T 47 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7292 (mt-10) REVERT: U 2 LYS cc_start: 0.6869 (mmmm) cc_final: 0.6527 (mmmm) REVERT: U 12 ILE cc_start: 0.9034 (pt) cc_final: 0.8599 (tt) REVERT: V 24 ARG cc_start: 0.8527 (ptp-110) cc_final: 0.8194 (ptp-110) REVERT: V 72 LYS cc_start: 0.6933 (mtmm) cc_final: 0.6261 (mptt) REVERT: V 91 GLN cc_start: 0.7852 (mp10) cc_final: 0.7209 (mp10) REVERT: V 92 HIS cc_start: 0.7741 (t-90) cc_final: 0.7422 (t70) REVERT: W 41 ARG cc_start: 0.7829 (ptp90) cc_final: 0.7015 (ptp-170) REVERT: X 17 SER cc_start: 0.9280 (t) cc_final: 0.8783 (p) REVERT: Y 30 PHE cc_start: 0.8589 (t80) cc_final: 0.8215 (t80) REVERT: Z 13 ILE cc_start: 0.8868 (mm) cc_final: 0.8635 (mm) REVERT: c 22 TRP cc_start: 0.5384 (p90) cc_final: 0.4635 (p90) REVERT: c 23 TYR cc_start: 0.4859 (t80) cc_final: 0.4411 (t80) REVERT: d 17 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6369 (m) REVERT: e 62 PHE cc_start: 0.7548 (m-80) cc_final: 0.7315 (m-10) REVERT: h 30 SER cc_start: 0.8124 (p) cc_final: 0.7838 (t) REVERT: h 105 ILE cc_start: 0.8069 (mt) cc_final: 0.7717 (mm) REVERT: i 116 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7501 (mmp80) REVERT: k 67 LYS cc_start: 0.7724 (pttt) cc_final: 0.7288 (tptt) REVERT: k 103 ARG cc_start: 0.6288 (mtt180) cc_final: 0.5403 (mmp80) REVERT: l 1 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.5219 (mmt) REVERT: l 66 TYR cc_start: 0.6766 (t80) cc_final: 0.6544 (t80) REVERT: m 90 LEU cc_start: 0.7079 (mt) cc_final: 0.6848 (mp) REVERT: p 9 ARG cc_start: 0.5590 (ttm-80) cc_final: 0.4901 (ttp80) REVERT: r 66 LEU cc_start: 0.8690 (mt) cc_final: 0.8341 (pp) REVERT: s 71 LEU cc_start: 0.7247 (mt) cc_final: 0.6820 (mm) REVERT: t 6 SER cc_start: 0.5981 (m) cc_final: 0.5670 (t) REVERT: t 25 LYS cc_start: 0.8756 (mttt) cc_final: 0.8468 (mtpp) outliers start: 112 outliers final: 105 residues processed: 1103 average time/residue: 1.3399 time to fit residues: 2483.9256 Evaluate side-chains 1158 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1049 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 6 residue 6 HIS Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 111 SER Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 107 TYR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 885 optimal weight: 0.9980 chunk 673 optimal weight: 20.0000 chunk 465 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 427 optimal weight: 5.9990 chunk 601 optimal weight: 5.9990 chunk 899 optimal weight: 0.4980 chunk 952 optimal weight: 20.0000 chunk 469 optimal weight: 6.9990 chunk 852 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 44 ASN 6 6 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.294 156395 Z= 0.321 Angle : 0.803 31.598 234908 Z= 0.394 Chirality : 0.038 0.747 30106 Planarity : 0.008 0.183 12132 Dihedral : 23.185 178.367 80755 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.17 % Favored : 90.62 % Rotamer: Outliers : 4.16 % Allowed : 15.09 % Favored : 80.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.11), residues: 5224 helix: -0.35 (0.12), residues: 1590 sheet: -1.29 (0.17), residues: 881 loop : -1.98 (0.11), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP S 48 HIS 0.068 0.002 HIS 6 6 PHE 0.048 0.003 PHE e 102 TYR 0.057 0.003 TYR T 73 ARG 0.026 0.001 ARG t 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1083 time to evaluate : 5.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 HIS cc_start: 0.6421 (m170) cc_final: 0.6220 (m170) REVERT: 1 52 ARG cc_start: 0.7103 (ptm160) cc_final: 0.6856 (ptm160) REVERT: 3 21 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7431 (tttt) REVERT: 3 22 ILE cc_start: 0.9098 (mt) cc_final: 0.8672 (mm) REVERT: 3 25 GLN cc_start: 0.8249 (tm-30) cc_final: 0.8042 (tm-30) REVERT: 3 30 ARG cc_start: 0.6624 (mmm160) cc_final: 0.6217 (mtp85) REVERT: 4 18 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8234 (mtp-110) REVERT: C 35 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8273 (tpp80) REVERT: C 101 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: C 192 THR cc_start: 0.8819 (m) cc_final: 0.8302 (p) REVERT: C 214 TRP cc_start: 0.8782 (m-10) cc_final: 0.7690 (m-10) REVERT: D 11 LEU cc_start: 0.8509 (mt) cc_final: 0.7978 (mp) REVERT: D 132 PHE cc_start: 0.8687 (m-10) cc_final: 0.8149 (m-10) REVERT: D 135 GLN cc_start: 0.8239 (mp10) cc_final: 0.7543 (mp10) REVERT: D 162 LYS cc_start: 0.8559 (tttt) cc_final: 0.8313 (tptt) REVERT: E 59 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8355 (mttm) REVERT: E 79 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8345 (mmm160) REVERT: E 123 ASP cc_start: 0.8245 (t70) cc_final: 0.7853 (t0) REVERT: E 127 ASN cc_start: 0.7519 (m-40) cc_final: 0.7127 (m-40) REVERT: E 157 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7674 (mpp80) REVERT: E 173 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8442 (mmmt) REVERT: E 178 LEU cc_start: 0.8870 (mt) cc_final: 0.8503 (mt) REVERT: F 37 THR cc_start: 0.6164 (t) cc_final: 0.5922 (t) REVERT: F 71 LYS cc_start: 0.8796 (tppt) cc_final: 0.7055 (tttt) REVERT: F 172 GLU cc_start: 0.8959 (mp0) cc_final: 0.8596 (mp0) REVERT: G 158 TYR cc_start: 0.6727 (m-10) cc_final: 0.6442 (m-10) REVERT: H 1 MET cc_start: 0.7044 (tpt) cc_final: 0.6341 (ttm) REVERT: H 23 ASP cc_start: 0.7604 (t0) cc_final: 0.7335 (t0) REVERT: H 27 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7535 (ttp-110) REVERT: J 57 ILE cc_start: 0.8530 (mm) cc_final: 0.8137 (mm) REVERT: J 61 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7992 (ptmm) REVERT: K 6 SER cc_start: 0.9244 (t) cc_final: 0.8878 (p) REVERT: K 107 ARG cc_start: 0.8279 (mmp80) cc_final: 0.6995 (mmp80) REVERT: K 112 MET cc_start: 0.7670 (tpt) cc_final: 0.7239 (tpp) REVERT: L 63 LEU cc_start: 0.9019 (tp) cc_final: 0.8811 (tp) REVERT: L 73 GLU cc_start: 0.7396 (tp30) cc_final: 0.7183 (tp30) REVERT: L 78 ASN cc_start: 0.7798 (t0) cc_final: 0.7500 (t0) REVERT: M 110 ASN cc_start: 0.6752 (t0) cc_final: 0.6458 (m-40) REVERT: M 111 GLU cc_start: 0.6597 (mp0) cc_final: 0.6385 (mp0) REVERT: M 132 ILE cc_start: 0.7715 (mt) cc_final: 0.7244 (tp) REVERT: N 27 SER cc_start: 0.9261 (m) cc_final: 0.8839 (p) REVERT: N 30 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7605 (tm-30) REVERT: N 34 ILE cc_start: 0.9389 (mm) cc_final: 0.8952 (mm) REVERT: N 103 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6237 (mtp180) REVERT: N 104 LYS cc_start: 0.7877 (ptmm) cc_final: 0.7672 (ptpp) REVERT: N 107 ASN cc_start: 0.8794 (t0) cc_final: 0.8482 (t0) REVERT: P 24 THR cc_start: 0.8826 (m) cc_final: 0.8555 (p) REVERT: P 70 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7805 (mm-30) REVERT: P 72 THR cc_start: 0.9012 (p) cc_final: 0.8744 (p) REVERT: Q 74 ILE cc_start: 0.8964 (tp) cc_final: 0.8676 (tt) REVERT: Q 102 ASP cc_start: 0.8114 (t0) cc_final: 0.7887 (t0) REVERT: R 34 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7713 (tm-30) REVERT: S 16 LYS cc_start: 0.8789 (pttt) cc_final: 0.8403 (pttm) REVERT: T 8 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7436 (tpp80) REVERT: T 39 LYS cc_start: 0.8710 (mttt) cc_final: 0.8246 (mtmm) REVERT: U 2 LYS cc_start: 0.6784 (mmmm) cc_final: 0.6390 (mmmm) REVERT: U 12 ILE cc_start: 0.9141 (pt) cc_final: 0.8730 (tt) REVERT: U 99 LYS cc_start: 0.4394 (tmtt) cc_final: 0.2710 (ptmm) REVERT: V 24 ARG cc_start: 0.8549 (ptp-110) cc_final: 0.8292 (ptp90) REVERT: V 72 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6355 (mtmm) REVERT: V 91 GLN cc_start: 0.7729 (mp10) cc_final: 0.7012 (mp10) REVERT: V 92 HIS cc_start: 0.7720 (t-90) cc_final: 0.7401 (t70) REVERT: X 17 SER cc_start: 0.9281 (t) cc_final: 0.8780 (p) REVERT: Y 30 PHE cc_start: 0.8638 (t80) cc_final: 0.8297 (t80) REVERT: Z 21 GLU cc_start: 0.7838 (mp0) cc_final: 0.7543 (mp0) REVERT: c 22 TRP cc_start: 0.5526 (p90) cc_final: 0.4753 (p90) REVERT: c 23 TYR cc_start: 0.5101 (t80) cc_final: 0.4499 (t80) REVERT: d 1 MET cc_start: 0.4760 (OUTLIER) cc_final: 0.4490 (ptm) REVERT: d 17 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6396 (m) REVERT: d 63 MET cc_start: 0.6690 (mmp) cc_final: 0.6456 (mmt) REVERT: d 67 PHE cc_start: 0.6951 (t80) cc_final: 0.6726 (t80) REVERT: e 62 PHE cc_start: 0.7583 (m-80) cc_final: 0.7352 (m-10) REVERT: e 183 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: h 30 SER cc_start: 0.8231 (p) cc_final: 0.7869 (t) REVERT: i 115 ASP cc_start: 0.6582 (t70) cc_final: 0.6249 (t0) REVERT: i 116 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7493 (mmp80) REVERT: k 66 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7383 (mmm-85) REVERT: k 67 LYS cc_start: 0.7635 (pttt) cc_final: 0.7159 (tptt) REVERT: l 1 MET cc_start: 0.5474 (mtt) cc_final: 0.4719 (mtt) REVERT: l 3 THR cc_start: 0.8251 (m) cc_final: 0.7905 (p) REVERT: l 66 TYR cc_start: 0.6757 (t80) cc_final: 0.6552 (t80) REVERT: m 15 MET cc_start: 0.7297 (tpt) cc_final: 0.7059 (tpt) REVERT: m 90 LEU cc_start: 0.7067 (mt) cc_final: 0.6810 (mp) REVERT: o 84 ARG cc_start: 0.6815 (ttm170) cc_final: 0.6572 (ttm170) REVERT: p 1 MET cc_start: 0.3063 (ttt) cc_final: 0.2082 (ttm) REVERT: p 9 ARG cc_start: 0.5590 (ttm-80) cc_final: 0.5025 (ttp80) REVERT: s 71 LEU cc_start: 0.7316 (mt) cc_final: 0.6913 (mm) REVERT: t 6 SER cc_start: 0.6203 (m) cc_final: 0.5844 (t) REVERT: t 25 LYS cc_start: 0.8749 (mttt) cc_final: 0.8443 (mtpp) outliers start: 181 outliers final: 134 residues processed: 1146 average time/residue: 1.3390 time to fit residues: 2572.7253 Evaluate side-chains 1154 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1012 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LYS Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 107 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 111 ARG Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 792 optimal weight: 0.9990 chunk 540 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 708 optimal weight: 10.0000 chunk 392 optimal weight: 0.9980 chunk 812 optimal weight: 20.0000 chunk 658 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 486 optimal weight: 1.9990 chunk 854 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 44 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 156395 Z= 0.320 Angle : 0.802 31.219 234908 Z= 0.393 Chirality : 0.038 0.733 30106 Planarity : 0.008 0.182 12132 Dihedral : 23.185 178.367 80755 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.17 % Favored : 90.62 % Rotamer: Outliers : 3.38 % Allowed : 16.43 % Favored : 80.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.11), residues: 5224 helix: -0.35 (0.12), residues: 1590 sheet: -1.29 (0.17), residues: 881 loop : -1.98 (0.11), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP S 48 HIS 0.064 0.002 HIS 6 6 PHE 0.052 0.003 PHE F 137 TYR 0.056 0.003 TYR T 73 ARG 0.025 0.001 ARG t 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1013 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 HIS cc_start: 0.6460 (m170) cc_final: 0.6219 (m170) REVERT: 1 52 ARG cc_start: 0.7110 (ptm160) cc_final: 0.6855 (ptm160) REVERT: 3 21 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7388 (tttt) REVERT: 3 22 ILE cc_start: 0.9099 (mt) cc_final: 0.8668 (mm) REVERT: 3 25 GLN cc_start: 0.8241 (tm-30) cc_final: 0.8039 (tm-30) REVERT: 3 30 ARG cc_start: 0.6608 (mmm160) cc_final: 0.6218 (mtp85) REVERT: 4 18 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.8234 (mtp-110) REVERT: C 35 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8273 (tpp80) REVERT: C 101 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: C 192 THR cc_start: 0.8816 (m) cc_final: 0.8300 (p) REVERT: C 214 TRP cc_start: 0.8788 (m-10) cc_final: 0.7690 (m-10) REVERT: C 263 SER cc_start: 0.9138 (m) cc_final: 0.8912 (t) REVERT: D 11 LEU cc_start: 0.8515 (mt) cc_final: 0.7978 (mp) REVERT: D 132 PHE cc_start: 0.8659 (m-10) cc_final: 0.8148 (m-10) REVERT: D 135 GLN cc_start: 0.8239 (mp10) cc_final: 0.7542 (mp10) REVERT: D 162 LYS cc_start: 0.8555 (tttt) cc_final: 0.8313 (tptt) REVERT: E 59 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8356 (mttm) REVERT: E 79 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8345 (mmm160) REVERT: E 123 ASP cc_start: 0.8247 (t70) cc_final: 0.7854 (t0) REVERT: E 127 ASN cc_start: 0.7528 (m-40) cc_final: 0.7128 (m-40) REVERT: E 157 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7674 (mpp80) REVERT: E 173 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8441 (mmmt) REVERT: E 178 LEU cc_start: 0.8870 (mt) cc_final: 0.8501 (mt) REVERT: F 37 THR cc_start: 0.6205 (t) cc_final: 0.5923 (t) REVERT: F 71 LYS cc_start: 0.8826 (tppt) cc_final: 0.7055 (tttt) REVERT: F 172 GLU cc_start: 0.8923 (mp0) cc_final: 0.8596 (mp0) REVERT: G 158 TYR cc_start: 0.6722 (m-10) cc_final: 0.6441 (m-10) REVERT: H 1 MET cc_start: 0.7039 (tpt) cc_final: 0.6339 (ttm) REVERT: H 23 ASP cc_start: 0.7596 (t0) cc_final: 0.7333 (t0) REVERT: H 27 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7535 (ttp-110) REVERT: J 57 ILE cc_start: 0.8539 (mm) cc_final: 0.8138 (mm) REVERT: J 61 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7992 (ptmm) REVERT: K 6 SER cc_start: 0.9246 (t) cc_final: 0.8878 (p) REVERT: K 107 ARG cc_start: 0.8294 (mmp80) cc_final: 0.6996 (mmp80) REVERT: K 112 MET cc_start: 0.7677 (tpt) cc_final: 0.7238 (tpp) REVERT: L 73 GLU cc_start: 0.7405 (tp30) cc_final: 0.7184 (tp30) REVERT: M 110 ASN cc_start: 0.6771 (t0) cc_final: 0.6461 (m-40) REVERT: M 111 GLU cc_start: 0.6605 (mp0) cc_final: 0.6383 (mp0) REVERT: N 27 SER cc_start: 0.9256 (m) cc_final: 0.8837 (p) REVERT: N 30 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7601 (tm-30) REVERT: N 34 ILE cc_start: 0.9368 (mm) cc_final: 0.8952 (mm) REVERT: N 103 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6238 (mtp180) REVERT: N 107 ASN cc_start: 0.8793 (t0) cc_final: 0.8482 (t0) REVERT: P 24 THR cc_start: 0.8834 (m) cc_final: 0.8555 (p) REVERT: P 70 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7805 (mm-30) REVERT: P 72 THR cc_start: 0.9011 (p) cc_final: 0.8752 (p) REVERT: Q 74 ILE cc_start: 0.8932 (tp) cc_final: 0.8676 (tt) REVERT: Q 102 ASP cc_start: 0.8110 (t0) cc_final: 0.7886 (t0) REVERT: R 34 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7711 (tm-30) REVERT: S 16 LYS cc_start: 0.8797 (pttt) cc_final: 0.8403 (pttm) REVERT: T 8 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7437 (tpp80) REVERT: T 39 LYS cc_start: 0.8691 (mttt) cc_final: 0.8246 (mtmm) REVERT: T 73 TYR cc_start: 0.8216 (m-10) cc_final: 0.8011 (m-10) REVERT: U 2 LYS cc_start: 0.6769 (mmmm) cc_final: 0.6397 (mmmm) REVERT: U 12 ILE cc_start: 0.9132 (pt) cc_final: 0.8730 (tt) REVERT: V 24 ARG cc_start: 0.8555 (ptp-110) cc_final: 0.8293 (ptp90) REVERT: V 72 LYS cc_start: 0.6858 (mtmm) cc_final: 0.6354 (mtmm) REVERT: V 91 GLN cc_start: 0.7651 (mp10) cc_final: 0.7018 (mp10) REVERT: V 92 HIS cc_start: 0.7737 (t-90) cc_final: 0.7400 (t70) REVERT: X 17 SER cc_start: 0.9284 (t) cc_final: 0.8780 (p) REVERT: Y 30 PHE cc_start: 0.8645 (t80) cc_final: 0.8297 (t80) REVERT: Z 21 GLU cc_start: 0.7833 (mp0) cc_final: 0.7544 (mp0) REVERT: c 22 TRP cc_start: 0.5580 (p90) cc_final: 0.4750 (p90) REVERT: c 23 TYR cc_start: 0.5076 (t80) cc_final: 0.4499 (t80) REVERT: d 1 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4498 (ptm) REVERT: d 17 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6397 (m) REVERT: d 63 MET cc_start: 0.6664 (mmp) cc_final: 0.6456 (mmt) REVERT: e 62 PHE cc_start: 0.7589 (m-80) cc_final: 0.7352 (m-10) REVERT: e 183 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: h 30 SER cc_start: 0.8243 (p) cc_final: 0.7868 (t) REVERT: h 130 TYR cc_start: 0.7917 (m-80) cc_final: 0.7159 (m-80) REVERT: i 115 ASP cc_start: 0.6578 (t70) cc_final: 0.6250 (t0) REVERT: i 116 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7493 (mmp80) REVERT: k 66 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7380 (mmm-85) REVERT: k 67 LYS cc_start: 0.7630 (pttt) cc_final: 0.7159 (tptt) REVERT: l 1 MET cc_start: 0.5472 (mtt) cc_final: 0.4712 (mtt) REVERT: l 3 THR cc_start: 0.8266 (m) cc_final: 0.7904 (p) REVERT: m 15 MET cc_start: 0.7293 (tpt) cc_final: 0.7059 (tpt) REVERT: m 90 LEU cc_start: 0.7064 (mt) cc_final: 0.6811 (mp) REVERT: p 1 MET cc_start: 0.3069 (ttt) cc_final: 0.2082 (ttm) REVERT: p 9 ARG cc_start: 0.5621 (ttm-80) cc_final: 0.5024 (ttp80) REVERT: s 71 LEU cc_start: 0.7304 (mt) cc_final: 0.6913 (mm) REVERT: t 6 SER cc_start: 0.6212 (m) cc_final: 0.5844 (t) REVERT: t 25 LYS cc_start: 0.8755 (mttt) cc_final: 0.8443 (mtpp) outliers start: 147 outliers final: 138 residues processed: 1062 average time/residue: 1.2935 time to fit residues: 2310.4604 Evaluate side-chains 1149 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1003 time to evaluate : 5.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LYS Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 107 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 111 ARG Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 320 optimal weight: 10.0000 chunk 857 optimal weight: 9.9990 chunk 188 optimal weight: 30.0000 chunk 558 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 953 optimal weight: 5.9990 chunk 791 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 500 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 44 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 156395 Z= 0.326 Angle : 0.799 29.563 234908 Z= 0.393 Chirality : 0.038 0.683 30106 Planarity : 0.008 0.180 12132 Dihedral : 23.185 178.358 80755 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.15 % Favored : 90.64 % Rotamer: Outliers : 3.70 % Allowed : 16.24 % Favored : 80.06 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.11), residues: 5224 helix: -0.35 (0.12), residues: 1591 sheet: -1.29 (0.17), residues: 881 loop : -1.98 (0.11), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP S 48 HIS 0.051 0.002 HIS 6 6 PHE 0.070 0.003 PHE F 137 TYR 0.055 0.003 TYR F 135 ARG 0.041 0.001 ARG S 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1004 time to evaluate : 5.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 HIS cc_start: 0.6457 (m170) cc_final: 0.6218 (m170) REVERT: 1 52 ARG cc_start: 0.7112 (ptm160) cc_final: 0.6865 (ptm160) REVERT: 3 21 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7393 (tttt) REVERT: 3 22 ILE cc_start: 0.9099 (mt) cc_final: 0.8675 (mm) REVERT: 3 30 ARG cc_start: 0.6607 (mmm160) cc_final: 0.6221 (mtp85) REVERT: 4 18 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.8235 (mtp-110) REVERT: C 35 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8272 (tpp80) REVERT: C 101 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: C 192 THR cc_start: 0.8814 (m) cc_final: 0.8302 (p) REVERT: C 214 TRP cc_start: 0.8789 (m-10) cc_final: 0.7694 (m-10) REVERT: C 263 SER cc_start: 0.9139 (m) cc_final: 0.8920 (t) REVERT: D 11 LEU cc_start: 0.8516 (mt) cc_final: 0.7980 (mp) REVERT: D 132 PHE cc_start: 0.8661 (m-10) cc_final: 0.8148 (m-10) REVERT: D 135 GLN cc_start: 0.8241 (mp10) cc_final: 0.7543 (mp10) REVERT: D 162 LYS cc_start: 0.8556 (tttt) cc_final: 0.8315 (tptt) REVERT: E 59 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8358 (mttm) REVERT: E 79 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8345 (mmm160) REVERT: E 123 ASP cc_start: 0.8248 (t70) cc_final: 0.7855 (t0) REVERT: E 127 ASN cc_start: 0.7528 (m-40) cc_final: 0.7128 (m-40) REVERT: E 157 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7678 (mpp80) REVERT: E 173 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8442 (mmmt) REVERT: E 178 LEU cc_start: 0.8868 (mt) cc_final: 0.8503 (mt) REVERT: F 37 THR cc_start: 0.6208 (t) cc_final: 0.5927 (t) REVERT: F 71 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7057 (tttt) REVERT: F 172 GLU cc_start: 0.8924 (mp0) cc_final: 0.8600 (mp0) REVERT: G 158 TYR cc_start: 0.6724 (m-10) cc_final: 0.6444 (m-10) REVERT: H 1 MET cc_start: 0.7038 (tpt) cc_final: 0.6343 (ttm) REVERT: H 23 ASP cc_start: 0.7594 (t0) cc_final: 0.7336 (t0) REVERT: H 27 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7536 (ttp-110) REVERT: J 57 ILE cc_start: 0.8541 (mm) cc_final: 0.8139 (mm) REVERT: J 61 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7993 (ptmm) REVERT: K 6 SER cc_start: 0.9247 (t) cc_final: 0.8878 (p) REVERT: K 107 ARG cc_start: 0.8295 (mmp80) cc_final: 0.6999 (mmp80) REVERT: K 112 MET cc_start: 0.7679 (tpt) cc_final: 0.7244 (tpp) REVERT: L 73 GLU cc_start: 0.7404 (tp30) cc_final: 0.7183 (tp30) REVERT: M 110 ASN cc_start: 0.6777 (t0) cc_final: 0.6462 (m-40) REVERT: M 111 GLU cc_start: 0.6609 (mp0) cc_final: 0.6386 (mp0) REVERT: N 27 SER cc_start: 0.9257 (m) cc_final: 0.8837 (p) REVERT: N 30 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7605 (tm-30) REVERT: N 34 ILE cc_start: 0.9365 (mm) cc_final: 0.8953 (mm) REVERT: N 103 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6238 (mtp180) REVERT: N 107 ASN cc_start: 0.8798 (t0) cc_final: 0.8483 (t0) REVERT: P 24 THR cc_start: 0.8834 (m) cc_final: 0.8556 (p) REVERT: P 70 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7807 (mm-30) REVERT: P 72 THR cc_start: 0.9011 (p) cc_final: 0.8752 (p) REVERT: Q 74 ILE cc_start: 0.8934 (tp) cc_final: 0.8675 (tt) REVERT: Q 102 ASP cc_start: 0.8110 (t0) cc_final: 0.7885 (t0) REVERT: R 34 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7712 (tm-30) REVERT: S 16 LYS cc_start: 0.8796 (pttt) cc_final: 0.8403 (pttm) REVERT: T 8 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7442 (tpp80) REVERT: T 39 LYS cc_start: 0.8692 (mttt) cc_final: 0.8247 (mtmm) REVERT: U 2 LYS cc_start: 0.6778 (mmmm) cc_final: 0.6397 (mmmm) REVERT: U 12 ILE cc_start: 0.9135 (pt) cc_final: 0.8734 (tt) REVERT: V 24 ARG cc_start: 0.8555 (ptp-110) cc_final: 0.8292 (ptp90) REVERT: V 72 LYS cc_start: 0.6859 (mtmm) cc_final: 0.6355 (mtmm) REVERT: V 91 GLN cc_start: 0.7660 (mp10) cc_final: 0.7018 (mp10) REVERT: V 92 HIS cc_start: 0.7738 (t-90) cc_final: 0.7400 (t70) REVERT: X 17 SER cc_start: 0.9285 (t) cc_final: 0.8776 (p) REVERT: X 29 TRP cc_start: 0.9090 (m-90) cc_final: 0.8846 (m-90) REVERT: Y 30 PHE cc_start: 0.8646 (t80) cc_final: 0.8301 (t80) REVERT: Z 21 GLU cc_start: 0.7834 (mp0) cc_final: 0.7543 (mp0) REVERT: c 22 TRP cc_start: 0.5574 (p90) cc_final: 0.4745 (p90) REVERT: c 23 TYR cc_start: 0.5079 (t80) cc_final: 0.4500 (t80) REVERT: d 1 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4498 (ptm) REVERT: d 17 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6398 (m) REVERT: d 63 MET cc_start: 0.6669 (mmp) cc_final: 0.6452 (mmt) REVERT: e 62 PHE cc_start: 0.7590 (m-80) cc_final: 0.7352 (m-10) REVERT: e 183 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: h 30 SER cc_start: 0.8245 (p) cc_final: 0.7869 (t) REVERT: h 130 TYR cc_start: 0.7928 (m-80) cc_final: 0.7176 (m-80) REVERT: i 115 ASP cc_start: 0.6579 (t70) cc_final: 0.6248 (t0) REVERT: i 116 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7494 (mmp80) REVERT: k 66 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7380 (mmm-85) REVERT: k 67 LYS cc_start: 0.7630 (pttt) cc_final: 0.7160 (tptt) REVERT: l 1 MET cc_start: 0.5473 (mtt) cc_final: 0.4692 (mtt) REVERT: l 3 THR cc_start: 0.8267 (m) cc_final: 0.7906 (p) REVERT: m 15 MET cc_start: 0.7292 (tpt) cc_final: 0.7055 (tpt) REVERT: m 90 LEU cc_start: 0.7066 (mt) cc_final: 0.6813 (mp) REVERT: p 1 MET cc_start: 0.3072 (ttt) cc_final: 0.2085 (ttm) REVERT: p 9 ARG cc_start: 0.5623 (ttm-80) cc_final: 0.5023 (ttp80) REVERT: s 71 LEU cc_start: 0.7303 (mt) cc_final: 0.6914 (mm) REVERT: t 6 SER cc_start: 0.6213 (m) cc_final: 0.5847 (t) REVERT: t 25 LYS cc_start: 0.8756 (mttt) cc_final: 0.8513 (mtpp) outliers start: 161 outliers final: 148 residues processed: 1059 average time/residue: 1.3375 time to fit residues: 2384.4491 Evaluate side-chains 1159 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1002 time to evaluate : 5.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 LYS Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 73 LYS Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 48 TRP Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 107 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 66 ARG Chi-restraints excluded: chain k residue 103 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 64 TYR Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 111 ARG Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 918 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 542 optimal weight: 0.9980 chunk 695 optimal weight: 20.0000 chunk 539 optimal weight: 0.0020 chunk 802 optimal weight: 7.9990 chunk 532 optimal weight: 1.9990 chunk 949 optimal weight: 6.9990 chunk 594 optimal weight: 6.9990 chunk 578 optimal weight: 6.9990 chunk 438 optimal weight: 9.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 44 ASN 3 31 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN J 136 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN W 19 GLN Y 35 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 HIS ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 156395 Z= 0.272 Angle : 0.761 35.594 234908 Z= 0.376 Chirality : 0.037 1.090 30106 Planarity : 0.007 0.128 12132 Dihedral : 23.165 178.085 80755 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.26 % Favored : 90.52 % Rotamer: Outliers : 3.95 % Allowed : 16.15 % Favored : 79.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.11), residues: 5224 helix: -0.27 (0.12), residues: 1580 sheet: -1.34 (0.17), residues: 900 loop : -1.98 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP p 80 HIS 0.037 0.002 HIS O 41 PHE 0.098 0.003 PHE F 137 TYR 0.090 0.003 TYR F 135 ARG 0.046 0.001 ARG q 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1058 time to evaluate : 7.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 HIS cc_start: 0.6537 (m170) cc_final: 0.6246 (m170) REVERT: 1 52 ARG cc_start: 0.7137 (ptm160) cc_final: 0.6866 (ptm160) REVERT: 3 21 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7379 (tttt) REVERT: 3 22 ILE cc_start: 0.9106 (mt) cc_final: 0.8689 (mm) REVERT: 3 30 ARG cc_start: 0.6686 (mmm160) cc_final: 0.6180 (mtp85) REVERT: C 35 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8244 (tpp80) REVERT: C 83 GLU cc_start: 0.8017 (mp0) cc_final: 0.7351 (mp0) REVERT: C 192 THR cc_start: 0.8825 (m) cc_final: 0.8315 (p) REVERT: C 214 TRP cc_start: 0.8866 (m-10) cc_final: 0.7904 (m-10) REVERT: C 263 SER cc_start: 0.9131 (m) cc_final: 0.8909 (t) REVERT: D 11 LEU cc_start: 0.8488 (mt) cc_final: 0.7930 (mp) REVERT: D 132 PHE cc_start: 0.8723 (m-10) cc_final: 0.8279 (m-10) REVERT: D 135 GLN cc_start: 0.8323 (mp10) cc_final: 0.7468 (mp10) REVERT: D 144 VAL cc_start: 0.8824 (m) cc_final: 0.7618 (m) REVERT: D 162 LYS cc_start: 0.8573 (tttt) cc_final: 0.8320 (tptt) REVERT: E 59 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8391 (mttm) REVERT: E 123 ASP cc_start: 0.8257 (t70) cc_final: 0.7908 (t0) REVERT: E 127 ASN cc_start: 0.7487 (m-40) cc_final: 0.7104 (m-40) REVERT: E 173 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8448 (mmmt) REVERT: E 178 LEU cc_start: 0.8902 (mt) cc_final: 0.8519 (mt) REVERT: F 40 LYS cc_start: 0.7053 (tptt) cc_final: 0.6762 (tptt) REVERT: F 43 VAL cc_start: 0.8084 (t) cc_final: 0.7818 (t) REVERT: F 71 LYS cc_start: 0.8850 (tppt) cc_final: 0.7060 (tttt) REVERT: F 103 MET cc_start: 0.7637 (ptm) cc_final: 0.7172 (ptm) REVERT: F 152 LYS cc_start: 0.7098 (mtmm) cc_final: 0.6753 (ptpt) REVERT: G 158 TYR cc_start: 0.6760 (m-10) cc_final: 0.6412 (m-10) REVERT: H 1 MET cc_start: 0.7052 (tpt) cc_final: 0.6353 (ttm) REVERT: H 27 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7622 (ttp-110) REVERT: J 43 THR cc_start: 0.9076 (p) cc_final: 0.8595 (t) REVERT: J 61 LYS cc_start: 0.8239 (tppt) cc_final: 0.7919 (ptmm) REVERT: J 67 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7831 (p0) REVERT: J 102 GLU cc_start: 0.8329 (tt0) cc_final: 0.8062 (mt-10) REVERT: J 136 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8324 (tm-30) REVERT: K 6 SER cc_start: 0.9262 (t) cc_final: 0.8866 (p) REVERT: K 107 ARG cc_start: 0.8337 (mmp80) cc_final: 0.7001 (mmp80) REVERT: K 112 MET cc_start: 0.7707 (tpt) cc_final: 0.7037 (mpp) REVERT: M 110 ASN cc_start: 0.6829 (t0) cc_final: 0.6393 (m-40) REVERT: N 27 SER cc_start: 0.9204 (m) cc_final: 0.8832 (p) REVERT: N 30 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7578 (tm-30) REVERT: N 34 ILE cc_start: 0.9401 (mm) cc_final: 0.8963 (mm) REVERT: N 103 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6301 (mtp180) REVERT: N 107 ASN cc_start: 0.8709 (t0) cc_final: 0.8404 (t0) REVERT: P 24 THR cc_start: 0.8839 (m) cc_final: 0.8599 (p) REVERT: P 60 VAL cc_start: 0.9214 (m) cc_final: 0.8886 (p) REVERT: P 72 THR cc_start: 0.8978 (p) cc_final: 0.8676 (p) REVERT: Q 74 ILE cc_start: 0.9022 (tp) cc_final: 0.8730 (tt) REVERT: Q 102 ASP cc_start: 0.8108 (t0) cc_final: 0.7907 (t0) REVERT: R 34 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7796 (tm-30) REVERT: S 16 LYS cc_start: 0.8794 (pttt) cc_final: 0.8411 (pttm) REVERT: S 100 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: T 8 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7483 (tpp80) REVERT: T 39 LYS cc_start: 0.8709 (mttt) cc_final: 0.8227 (mtmm) REVERT: T 53 LYS cc_start: 0.6764 (tmtt) cc_final: 0.6334 (tptt) REVERT: U 12 ILE cc_start: 0.9176 (pt) cc_final: 0.8806 (tt) REVERT: V 72 LYS cc_start: 0.6723 (mtmm) cc_final: 0.6233 (mtmm) REVERT: V 91 GLN cc_start: 0.7671 (mt0) cc_final: 0.7339 (mm-40) REVERT: V 92 HIS cc_start: 0.7724 (t-90) cc_final: 0.7427 (t70) REVERT: X 17 SER cc_start: 0.9309 (t) cc_final: 0.8767 (p) REVERT: Y 30 PHE cc_start: 0.8643 (t80) cc_final: 0.8417 (t80) REVERT: c 22 TRP cc_start: 0.5669 (p90) cc_final: 0.4802 (p90) REVERT: c 23 TYR cc_start: 0.5222 (t80) cc_final: 0.4669 (t80) REVERT: d 53 LYS cc_start: 0.6041 (ttpt) cc_final: 0.5831 (ttpt) REVERT: e 62 PHE cc_start: 0.7580 (m-80) cc_final: 0.7361 (m-10) REVERT: e 183 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: i 115 ASP cc_start: 0.6759 (t70) cc_final: 0.6259 (t0) REVERT: i 116 ARG cc_start: 0.7828 (ttt180) cc_final: 0.7458 (mmp80) REVERT: l 1 MET cc_start: 0.5648 (mtt) cc_final: 0.5147 (mtt) REVERT: m 90 LEU cc_start: 0.7081 (mt) cc_final: 0.6845 (mp) REVERT: o 10 GLU cc_start: 0.7424 (pp20) cc_final: 0.7067 (pp20) REVERT: p 9 ARG cc_start: 0.5654 (ttm-80) cc_final: 0.5320 (ttp80) REVERT: p 68 GLU cc_start: 0.7220 (mp0) cc_final: 0.6409 (mm-30) REVERT: q 116 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5516 (pp20) REVERT: s 71 LEU cc_start: 0.7278 (mt) cc_final: 0.6867 (mm) REVERT: t 6 SER cc_start: 0.6086 (m) cc_final: 0.5740 (t) REVERT: t 25 LYS cc_start: 0.8889 (mttt) cc_final: 0.8568 (mtpp) outliers start: 172 outliers final: 137 residues processed: 1120 average time/residue: 1.3608 time to fit residues: 2573.6208 Evaluate side-chains 1145 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1004 time to evaluate : 5.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 PHE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 100 GLN Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 94 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 103 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 587 optimal weight: 9.9990 chunk 379 optimal weight: 10.0000 chunk 567 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 186 optimal weight: 50.0000 chunk 183 optimal weight: 70.0000 chunk 603 optimal weight: 9.9990 chunk 646 optimal weight: 20.0000 chunk 469 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 746 optimal weight: 30.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 44 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS l 5 GLN ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 156395 Z= 0.272 Angle : 0.761 35.593 234908 Z= 0.376 Chirality : 0.037 1.090 30106 Planarity : 0.007 0.128 12132 Dihedral : 23.165 178.085 80755 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.26 % Favored : 90.52 % Rotamer: Outliers : 3.29 % Allowed : 17.14 % Favored : 79.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.11), residues: 5224 helix: -0.27 (0.12), residues: 1580 sheet: -1.34 (0.17), residues: 900 loop : -1.98 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP p 80 HIS 0.037 0.002 HIS O 41 PHE 0.098 0.003 PHE F 137 TYR 0.090 0.003 TYR F 135 ARG 0.046 0.001 ARG q 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1005 time to evaluate : 5.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 52 ARG cc_start: 0.7128 (ptm160) cc_final: 0.6866 (ptm160) REVERT: 3 21 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7379 (tttt) REVERT: 3 22 ILE cc_start: 0.9112 (mt) cc_final: 0.8689 (mm) REVERT: 3 30 ARG cc_start: 0.6694 (mmm160) cc_final: 0.6180 (mtp85) REVERT: C 35 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8245 (tpp80) REVERT: C 83 GLU cc_start: 0.8009 (mp0) cc_final: 0.7351 (mp0) REVERT: C 192 THR cc_start: 0.8828 (m) cc_final: 0.8315 (p) REVERT: C 214 TRP cc_start: 0.8844 (m-10) cc_final: 0.7903 (m-10) REVERT: C 263 SER cc_start: 0.9131 (m) cc_final: 0.8909 (t) REVERT: D 11 LEU cc_start: 0.8491 (mt) cc_final: 0.7930 (mp) REVERT: D 132 PHE cc_start: 0.8718 (m-10) cc_final: 0.8279 (m-10) REVERT: D 135 GLN cc_start: 0.8321 (mp10) cc_final: 0.7469 (mp10) REVERT: D 144 VAL cc_start: 0.8822 (m) cc_final: 0.7619 (m) REVERT: D 162 LYS cc_start: 0.8570 (tttt) cc_final: 0.8320 (tptt) REVERT: E 59 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8390 (mttm) REVERT: E 123 ASP cc_start: 0.8255 (t70) cc_final: 0.7908 (t0) REVERT: E 127 ASN cc_start: 0.7490 (m-40) cc_final: 0.7105 (m-40) REVERT: E 173 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8447 (mmmt) REVERT: E 178 LEU cc_start: 0.8900 (mt) cc_final: 0.8519 (mt) REVERT: F 43 VAL cc_start: 0.8060 (t) cc_final: 0.7818 (t) REVERT: F 71 LYS cc_start: 0.8850 (tppt) cc_final: 0.7060 (tttt) REVERT: F 103 MET cc_start: 0.7470 (ptm) cc_final: 0.7171 (ptm) REVERT: F 152 LYS cc_start: 0.7118 (mtmm) cc_final: 0.6754 (ptpt) REVERT: G 158 TYR cc_start: 0.6757 (m-10) cc_final: 0.6412 (m-10) REVERT: H 1 MET cc_start: 0.7082 (tpt) cc_final: 0.6353 (ttm) REVERT: J 43 THR cc_start: 0.9001 (p) cc_final: 0.8595 (t) REVERT: J 61 LYS cc_start: 0.8238 (tppt) cc_final: 0.7919 (ptmm) REVERT: J 67 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7830 (p0) REVERT: J 136 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8324 (tm-30) REVERT: K 6 SER cc_start: 0.9260 (t) cc_final: 0.8866 (p) REVERT: K 107 ARG cc_start: 0.8336 (mmp80) cc_final: 0.7001 (mmp80) REVERT: K 112 MET cc_start: 0.7702 (tpt) cc_final: 0.7039 (mpp) REVERT: M 110 ASN cc_start: 0.6666 (t0) cc_final: 0.6393 (m-40) REVERT: N 27 SER cc_start: 0.9219 (m) cc_final: 0.8831 (p) REVERT: N 30 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7578 (tm-30) REVERT: N 34 ILE cc_start: 0.9352 (mm) cc_final: 0.8963 (mm) REVERT: N 103 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: N 107 ASN cc_start: 0.8721 (t0) cc_final: 0.8403 (t0) REVERT: P 24 THR cc_start: 0.8836 (m) cc_final: 0.8599 (p) REVERT: P 72 THR cc_start: 0.8979 (p) cc_final: 0.8678 (p) REVERT: Q 74 ILE cc_start: 0.9021 (tp) cc_final: 0.8730 (tt) REVERT: Q 102 ASP cc_start: 0.8151 (t0) cc_final: 0.7906 (t0) REVERT: R 34 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7796 (tm-30) REVERT: S 16 LYS cc_start: 0.8803 (pttt) cc_final: 0.8411 (pttm) REVERT: S 100 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: T 8 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7484 (tpp80) REVERT: T 39 LYS cc_start: 0.8707 (mttt) cc_final: 0.8226 (mtmm) REVERT: T 53 LYS cc_start: 0.6748 (tmtt) cc_final: 0.6332 (tptt) REVERT: U 2 LYS cc_start: 0.6609 (mmmm) cc_final: 0.6199 (mmmm) REVERT: U 12 ILE cc_start: 0.9191 (pt) cc_final: 0.8807 (tt) REVERT: V 72 LYS cc_start: 0.6717 (mtmm) cc_final: 0.6233 (mtmm) REVERT: V 92 HIS cc_start: 0.7749 (t-90) cc_final: 0.7428 (t70) REVERT: X 17 SER cc_start: 0.9302 (t) cc_final: 0.8767 (p) REVERT: Y 30 PHE cc_start: 0.8669 (t80) cc_final: 0.8416 (t80) REVERT: c 22 TRP cc_start: 0.5722 (p90) cc_final: 0.4801 (p90) REVERT: c 23 TYR cc_start: 0.5319 (t80) cc_final: 0.4669 (t80) REVERT: d 53 LYS cc_start: 0.6070 (ttpt) cc_final: 0.5830 (ttpt) REVERT: e 62 PHE cc_start: 0.7576 (m-80) cc_final: 0.7361 (m-10) REVERT: e 183 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: i 115 ASP cc_start: 0.6755 (t70) cc_final: 0.6259 (t0) REVERT: i 116 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7458 (mmp80) REVERT: l 1 MET cc_start: 0.5649 (mtt) cc_final: 0.5146 (mtt) REVERT: m 90 LEU cc_start: 0.7089 (mt) cc_final: 0.6845 (mp) REVERT: o 10 GLU cc_start: 0.7420 (pp20) cc_final: 0.7067 (pp20) REVERT: p 9 ARG cc_start: 0.5728 (ttm-80) cc_final: 0.5320 (ttp80) REVERT: p 68 GLU cc_start: 0.7210 (mp0) cc_final: 0.6409 (mm-30) REVERT: q 116 GLU cc_start: 0.6011 (tm-30) cc_final: 0.5514 (pp20) REVERT: s 71 LEU cc_start: 0.7262 (mt) cc_final: 0.6868 (mm) REVERT: t 6 SER cc_start: 0.6092 (m) cc_final: 0.5740 (t) REVERT: t 25 LYS cc_start: 0.8864 (mttt) cc_final: 0.8568 (mtpp) outliers start: 143 outliers final: 137 residues processed: 1056 average time/residue: 1.4238 time to fit residues: 2557.6238 Evaluate side-chains 1143 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1002 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 PHE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 100 GLN Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 94 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 103 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 863 optimal weight: 10.0000 chunk 909 optimal weight: 0.7980 chunk 829 optimal weight: 2.9990 chunk 884 optimal weight: 3.9990 chunk 532 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 chunk 694 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 799 optimal weight: 4.9990 chunk 836 optimal weight: 0.0000 chunk 881 optimal weight: 1.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS ** 1 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS l 5 GLN ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 156395 Z= 0.272 Angle : 0.761 35.593 234908 Z= 0.376 Chirality : 0.037 1.090 30106 Planarity : 0.007 0.128 12132 Dihedral : 23.165 178.085 80755 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.26 % Favored : 90.52 % Rotamer: Outliers : 3.29 % Allowed : 17.09 % Favored : 79.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.11), residues: 5224 helix: -0.27 (0.12), residues: 1580 sheet: -1.34 (0.17), residues: 900 loop : -1.98 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP p 80 HIS 0.037 0.002 HIS O 41 PHE 0.098 0.003 PHE F 137 TYR 0.090 0.003 TYR F 135 ARG 0.046 0.001 ARG q 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1002 time to evaluate : 5.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 52 ARG cc_start: 0.7129 (ptm160) cc_final: 0.6866 (ptm160) REVERT: 3 21 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7379 (tttt) REVERT: 3 22 ILE cc_start: 0.9112 (mt) cc_final: 0.8689 (mm) REVERT: 3 30 ARG cc_start: 0.6686 (mmm160) cc_final: 0.6180 (mtp85) REVERT: C 35 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8244 (tpp80) REVERT: C 83 GLU cc_start: 0.8009 (mp0) cc_final: 0.7352 (mp0) REVERT: C 192 THR cc_start: 0.8827 (m) cc_final: 0.8315 (p) REVERT: C 214 TRP cc_start: 0.8842 (m-10) cc_final: 0.7905 (m-10) REVERT: C 263 SER cc_start: 0.9132 (m) cc_final: 0.8909 (t) REVERT: D 11 LEU cc_start: 0.8493 (mt) cc_final: 0.7930 (mp) REVERT: D 132 PHE cc_start: 0.8719 (m-10) cc_final: 0.8279 (m-10) REVERT: D 135 GLN cc_start: 0.8321 (mp10) cc_final: 0.7469 (mp10) REVERT: D 144 VAL cc_start: 0.8824 (m) cc_final: 0.7619 (m) REVERT: D 162 LYS cc_start: 0.8571 (tttt) cc_final: 0.8320 (tptt) REVERT: E 59 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8390 (mttm) REVERT: E 123 ASP cc_start: 0.8254 (t70) cc_final: 0.7908 (t0) REVERT: E 127 ASN cc_start: 0.7491 (m-40) cc_final: 0.7105 (m-40) REVERT: E 173 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8447 (mmmt) REVERT: E 178 LEU cc_start: 0.8900 (mt) cc_final: 0.8519 (mt) REVERT: F 43 VAL cc_start: 0.8062 (t) cc_final: 0.7818 (t) REVERT: F 71 LYS cc_start: 0.8852 (tppt) cc_final: 0.7060 (tttt) REVERT: F 103 MET cc_start: 0.7456 (ptm) cc_final: 0.7171 (ptm) REVERT: F 152 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6754 (ptpt) REVERT: G 158 TYR cc_start: 0.6756 (m-10) cc_final: 0.6412 (m-10) REVERT: H 1 MET cc_start: 0.7103 (tpt) cc_final: 0.6353 (ttm) REVERT: J 43 THR cc_start: 0.9000 (p) cc_final: 0.8595 (t) REVERT: J 61 LYS cc_start: 0.8238 (tppt) cc_final: 0.7919 (ptmm) REVERT: J 67 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7830 (p0) REVERT: J 136 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8324 (tm-30) REVERT: K 6 SER cc_start: 0.9259 (t) cc_final: 0.8866 (p) REVERT: K 107 ARG cc_start: 0.8336 (mmp80) cc_final: 0.7001 (mmp80) REVERT: K 112 MET cc_start: 0.7704 (tpt) cc_final: 0.7039 (mpp) REVERT: M 110 ASN cc_start: 0.6667 (t0) cc_final: 0.6393 (m-40) REVERT: N 27 SER cc_start: 0.9219 (m) cc_final: 0.8832 (p) REVERT: N 30 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7578 (tm-30) REVERT: N 34 ILE cc_start: 0.9353 (mm) cc_final: 0.8963 (mm) REVERT: N 103 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: N 107 ASN cc_start: 0.8721 (t0) cc_final: 0.8404 (t0) REVERT: P 24 THR cc_start: 0.8846 (m) cc_final: 0.8599 (p) REVERT: P 72 THR cc_start: 0.8990 (p) cc_final: 0.8678 (p) REVERT: Q 74 ILE cc_start: 0.9021 (tp) cc_final: 0.8730 (tt) REVERT: Q 102 ASP cc_start: 0.8151 (t0) cc_final: 0.7907 (t0) REVERT: R 34 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7796 (tm-30) REVERT: S 16 LYS cc_start: 0.8803 (pttt) cc_final: 0.8411 (pttm) REVERT: S 100 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: T 8 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7485 (tpp80) REVERT: T 39 LYS cc_start: 0.8705 (mttt) cc_final: 0.8226 (mtmm) REVERT: T 53 LYS cc_start: 0.6745 (tmtt) cc_final: 0.6333 (tptt) REVERT: T 66 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.8081 (ttt-90) REVERT: U 2 LYS cc_start: 0.6609 (mmmm) cc_final: 0.6199 (mmmm) REVERT: U 12 ILE cc_start: 0.9192 (pt) cc_final: 0.8806 (tt) REVERT: V 72 LYS cc_start: 0.6715 (mtmm) cc_final: 0.6233 (mtmm) REVERT: V 92 HIS cc_start: 0.7757 (t-90) cc_final: 0.7428 (t70) REVERT: X 17 SER cc_start: 0.9301 (t) cc_final: 0.8767 (p) REVERT: Y 30 PHE cc_start: 0.8666 (t80) cc_final: 0.8418 (t80) REVERT: c 22 TRP cc_start: 0.5721 (p90) cc_final: 0.4801 (p90) REVERT: c 23 TYR cc_start: 0.5317 (t80) cc_final: 0.4670 (t80) REVERT: d 53 LYS cc_start: 0.6070 (ttpt) cc_final: 0.5831 (ttpt) REVERT: e 62 PHE cc_start: 0.7576 (m-80) cc_final: 0.7361 (m-10) REVERT: e 183 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: i 115 ASP cc_start: 0.6757 (t70) cc_final: 0.6258 (t0) REVERT: i 116 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7458 (mmp80) REVERT: l 1 MET cc_start: 0.5648 (mtt) cc_final: 0.5146 (mtt) REVERT: m 90 LEU cc_start: 0.7090 (mt) cc_final: 0.6845 (mp) REVERT: o 10 GLU cc_start: 0.7420 (pp20) cc_final: 0.7066 (pp20) REVERT: p 9 ARG cc_start: 0.5728 (ttm-80) cc_final: 0.5320 (ttp80) REVERT: p 68 GLU cc_start: 0.7211 (mp0) cc_final: 0.6409 (mm-30) REVERT: q 116 GLU cc_start: 0.6011 (tm-30) cc_final: 0.5514 (pp20) REVERT: s 71 LEU cc_start: 0.7263 (mt) cc_final: 0.6868 (mm) REVERT: t 6 SER cc_start: 0.6092 (m) cc_final: 0.5740 (t) REVERT: t 25 LYS cc_start: 0.8864 (mttt) cc_final: 0.8568 (mtpp) outliers start: 143 outliers final: 137 residues processed: 1053 average time/residue: 1.4081 time to fit residues: 2521.2565 Evaluate side-chains 1143 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1002 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 57 HIS Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 PHE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 100 GLN Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 94 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 103 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 60 THR Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain x residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 580 optimal weight: 0.0670 chunk 935 optimal weight: 10.0000 chunk 570 optimal weight: 4.9990 chunk 443 optimal weight: 20.0000 chunk 650 optimal weight: 20.0000 chunk 981 optimal weight: 6.9990 chunk 903 optimal weight: 10.0000 chunk 781 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 603 optimal weight: 9.9990 chunk 479 optimal weight: 10.0000 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 20 HIS 1 44 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN G 75 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 HIS Y 35 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 62 ASN k 32 HIS ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.185 156395 Z= 0.367 Angle : 0.824 33.618 234908 Z= 0.406 Chirality : 0.040 0.541 30106 Planarity : 0.007 0.171 12132 Dihedral : 23.115 177.385 80755 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.67 % Favored : 90.16 % Rotamer: Outliers : 3.51 % Allowed : 16.84 % Favored : 79.65 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.11), residues: 5224 helix: -0.30 (0.12), residues: 1575 sheet: -1.47 (0.16), residues: 896 loop : -2.05 (0.11), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP S 48 HIS 0.045 0.003 HIS L 57 PHE 0.062 0.003 PHE e 102 TYR 0.055 0.003 TYR F 135 ARG 0.063 0.001 ARG O 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10448 Ramachandran restraints generated. 5224 Oldfield, 0 Emsley, 5224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1033 time to evaluate : 5.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7398 (tttt) REVERT: 3 22 ILE cc_start: 0.9145 (mt) cc_final: 0.8736 (mm) REVERT: 3 30 ARG cc_start: 0.6798 (mmm160) cc_final: 0.6287 (mtp85) REVERT: 4 18 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8367 (mtp-110) REVERT: 4 24 MET cc_start: 0.7637 (mmm) cc_final: 0.7190 (mmm) REVERT: C 35 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8192 (tpp80) REVERT: C 192 THR cc_start: 0.8838 (m) cc_final: 0.8285 (p) REVERT: C 212 MET cc_start: 0.8291 (mmm) cc_final: 0.8045 (mmm) REVERT: C 214 TRP cc_start: 0.8936 (m-10) cc_final: 0.7982 (m-10) REVERT: D 24 VAL cc_start: 0.8600 (t) cc_final: 0.8355 (p) REVERT: D 132 PHE cc_start: 0.8816 (m-10) cc_final: 0.8320 (m-10) REVERT: D 135 GLN cc_start: 0.8557 (mp10) cc_final: 0.7628 (mp10) REVERT: D 144 VAL cc_start: 0.8857 (m) cc_final: 0.7643 (m) REVERT: D 162 LYS cc_start: 0.8577 (tttt) cc_final: 0.8338 (tptt) REVERT: E 59 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8483 (mttm) REVERT: E 123 ASP cc_start: 0.8313 (t70) cc_final: 0.7830 (t0) REVERT: E 127 ASN cc_start: 0.7500 (m-40) cc_final: 0.7092 (m-40) REVERT: E 173 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8416 (mmmt) REVERT: E 178 LEU cc_start: 0.8898 (mt) cc_final: 0.8541 (mt) REVERT: F 71 LYS cc_start: 0.8862 (tppt) cc_final: 0.7084 (tttt) REVERT: G 82 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: G 158 TYR cc_start: 0.6978 (m-10) cc_final: 0.6596 (m-10) REVERT: H 1 MET cc_start: 0.7100 (tpt) cc_final: 0.6374 (ttm) REVERT: J 43 THR cc_start: 0.9034 (p) cc_final: 0.8627 (t) REVERT: J 61 LYS cc_start: 0.8214 (tppt) cc_final: 0.8006 (ptmm) REVERT: J 67 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7814 (p0) REVERT: J 129 GLU cc_start: 0.7715 (pm20) cc_final: 0.7498 (pm20) REVERT: J 136 GLN cc_start: 0.8407 (tp-100) cc_final: 0.7710 (tm-30) REVERT: K 6 SER cc_start: 0.9355 (t) cc_final: 0.8972 (p) REVERT: K 107 ARG cc_start: 0.8403 (mmp80) cc_final: 0.6921 (mmp80) REVERT: K 112 MET cc_start: 0.7770 (tpt) cc_final: 0.6931 (mpp) REVERT: M 83 MET cc_start: 0.7715 (tpp) cc_final: 0.7514 (tpp) REVERT: M 105 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7178 (mt-10) REVERT: M 110 ASN cc_start: 0.6886 (t0) cc_final: 0.6553 (m-40) REVERT: M 111 GLU cc_start: 0.6729 (mp0) cc_final: 0.6446 (mp0) REVERT: N 27 SER cc_start: 0.9251 (m) cc_final: 0.8933 (p) REVERT: N 30 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7670 (tm-30) REVERT: N 34 ILE cc_start: 0.9361 (mm) cc_final: 0.8982 (mm) REVERT: N 107 ASN cc_start: 0.8823 (t0) cc_final: 0.8508 (t0) REVERT: P 24 THR cc_start: 0.8907 (m) cc_final: 0.8458 (p) REVERT: P 55 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8472 (mtt180) REVERT: P 72 THR cc_start: 0.9061 (p) cc_final: 0.8797 (p) REVERT: Q 30 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8267 (mtt-85) REVERT: Q 74 ILE cc_start: 0.8986 (tp) cc_final: 0.8727 (tt) REVERT: Q 102 ASP cc_start: 0.8196 (t0) cc_final: 0.7958 (t0) REVERT: R 5 TYR cc_start: 0.7606 (p90) cc_final: 0.7366 (p90) REVERT: R 34 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7862 (tm-30) REVERT: S 16 LYS cc_start: 0.8864 (pttt) cc_final: 0.8434 (pttm) REVERT: T 39 LYS cc_start: 0.8856 (mttt) cc_final: 0.8301 (mtmm) REVERT: T 47 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7418 (mt-10) REVERT: T 53 LYS cc_start: 0.6927 (tmtt) cc_final: 0.6601 (tptt) REVERT: T 66 ARG cc_start: 0.8491 (ttp-170) cc_final: 0.8072 (ttt-90) REVERT: T 73 TYR cc_start: 0.8687 (m-80) cc_final: 0.8024 (m-10) REVERT: U 2 LYS cc_start: 0.6734 (mmmm) cc_final: 0.6321 (mmmm) REVERT: U 12 ILE cc_start: 0.9168 (pt) cc_final: 0.8782 (tt) REVERT: V 24 ARG cc_start: 0.8646 (ptp-110) cc_final: 0.8141 (ptp-110) REVERT: V 72 LYS cc_start: 0.6793 (mtmm) cc_final: 0.6309 (mtmm) REVERT: V 78 THR cc_start: 0.9090 (m) cc_final: 0.8784 (p) REVERT: V 91 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8103 (mm-40) REVERT: V 92 HIS cc_start: 0.7971 (t-90) cc_final: 0.7571 (t70) REVERT: Z 21 GLU cc_start: 0.8083 (mp0) cc_final: 0.7874 (mp0) REVERT: c 22 TRP cc_start: 0.5790 (p90) cc_final: 0.4837 (p90) REVERT: c 23 TYR cc_start: 0.5428 (t80) cc_final: 0.4720 (t80) REVERT: d 53 LYS cc_start: 0.6286 (ttpt) cc_final: 0.5978 (ttpt) REVERT: e 183 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: f 7 MET cc_start: 0.6972 (tmm) cc_final: 0.6633 (tmm) REVERT: i 115 ASP cc_start: 0.6797 (t70) cc_final: 0.6270 (t0) REVERT: i 116 ARG cc_start: 0.7862 (ttt180) cc_final: 0.7494 (mmp80) REVERT: k 67 LYS cc_start: 0.7635 (pttt) cc_final: 0.7201 (tptt) REVERT: l 1 MET cc_start: 0.5785 (mtt) cc_final: 0.5117 (mtt) REVERT: m 90 LEU cc_start: 0.7185 (mt) cc_final: 0.6938 (mp) REVERT: o 21 ASP cc_start: 0.4072 (t0) cc_final: 0.3766 (m-30) REVERT: p 68 GLU cc_start: 0.7265 (mp0) cc_final: 0.6505 (mm-30) REVERT: q 92 ARG cc_start: 0.5585 (ptm160) cc_final: 0.5137 (ptm160) REVERT: q 96 LYS cc_start: 0.7174 (mppt) cc_final: 0.6708 (mppt) REVERT: q 116 GLU cc_start: 0.6004 (tm-30) cc_final: 0.5644 (pp20) REVERT: s 71 LEU cc_start: 0.7257 (mt) cc_final: 0.6871 (mm) REVERT: t 6 SER cc_start: 0.6277 (m) cc_final: 0.5937 (t) REVERT: t 25 LYS cc_start: 0.8764 (mttt) cc_final: 0.8246 (mtpp) outliers start: 153 outliers final: 126 residues processed: 1093 average time/residue: 1.3509 time to fit residues: 2475.9685 Evaluate side-chains 1119 residues out of total 4353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 990 time to evaluate : 4.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 54 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 20 HIS Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 ARG Chi-restraints excluded: chain 1 residue 45 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 53 ASN Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain J residue 22 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 44 ASN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 PHE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 24 LEU Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 35 GLU Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 48 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 94 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 130 TYR Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 76 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 103 ARG Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 72 HIS Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 40 TYR Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 95 LYS Chi-restraints excluded: chain q residue 120 LEU Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 985 random chunks: chunk 620 optimal weight: 4.9990 chunk 832 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 720 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 782 optimal weight: 3.9990 chunk 327 optimal weight: 20.0000 chunk 803 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 144 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 HIS l 5 GLN ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 60 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.127914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105670 restraints weight = 441059.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105478 restraints weight = 259322.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106165 restraints weight = 205412.043| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.191 156395 Z= 0.359 Angle : 0.816 41.504 234908 Z= 0.407 Chirality : 0.039 0.472 30106 Planarity : 0.007 0.132 12132 Dihedral : 23.116 177.464 80755 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.31 % Rotamer: Outliers : 3.33 % Allowed : 17.73 % Favored : 78.93 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.11), residues: 5224 helix: -0.29 (0.12), residues: 1581 sheet: -1.47 (0.16), residues: 892 loop : -2.06 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP S 48 HIS 0.071 0.003 HIS 1 20 PHE 0.079 0.003 PHE Y 30 TYR 0.052 0.003 TYR F 135 ARG 0.041 0.001 ARG q 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34453.21 seconds wall clock time: 604 minutes 44.86 seconds (36284.86 seconds total)