Starting phenix.real_space_refine on Wed Feb 21 13:01:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/02_2024/7as8_11889_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/02_2024/7as8_11889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/02_2024/7as8_11889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/02_2024/7as8_11889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/02_2024/7as8_11889_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/02_2024/7as8_11889_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 2994 5.49 5 S 102 5.16 5 C 47150 2.51 5 N 17428 2.21 5 O 26127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 93801 Number of models: 1 Model: "" Number of chains: 33 Chain: "0" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3993 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "1" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "2" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1563 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 30} Link IDs: {'rna2p': 15, 'rna3p': 57} Chain breaks: 2 Chain: "A" Number of atoms: 60389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2812, 60389 Inner-chain residues flagged as termini: ['pdbres=" G A1220 "'] Classifications: {'RNA': 2812} Modifications used: {'5*END': 2, 'rna2p_pur': 282, 'rna2p_pyr': 143, 'rna3p_pur': 1352, 'rna3p_pyr': 1035} Link IDs: {'rna2p': 425, 'rna3p': 2386} Chain breaks: 6 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "G" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "H" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 974 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 10, 'TRANS': 121} Chain: "L" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 2 Chain: "N" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "O" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "Q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "R" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "S" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "T" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "U" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "V" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "W" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "X" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "a" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 624 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "c" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "f" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "g" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "h" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "j" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 38.93, per 1000 atoms: 0.42 Number of scatterers: 93801 At special positions: 0 Unit cell: (223.04, 245.18, 223.04, 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 102 16.00 P 2994 15.00 O 26127 8.00 N 17428 7.00 C 47150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS f 30 " - pdb=" SG CYS f 43 " distance=2.03 Simple disulfide: pdb=" SG CYS f 33 " - pdb=" SG CYS f 46 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.25 Conformation dependent library (CDL) restraints added in 4.7 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6988 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 53 sheets defined 31.9% alpha, 19.4% beta 1019 base pairs and 1614 stacking pairs defined. Time for finding SS restraints: 32.52 Creating SS restraints... Processing helix chain '0' and resid 4 through 17 Processing helix chain '0' and resid 73 through 84 removed outlier: 3.556A pdb=" N GLU 0 84 " --> pdb=" O ARG 0 80 " (cutoff:3.500A) Processing helix chain '0' and resid 147 through 151 removed outlier: 3.672A pdb=" N MET 0 150 " --> pdb=" O SER 0 147 " (cutoff:3.500A) Processing helix chain '0' and resid 180 through 185 Processing helix chain '0' and resid 186 through 190 removed outlier: 3.700A pdb=" N GLY 0 190 " --> pdb=" O PHE 0 187 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 196 removed outlier: 3.999A pdb=" N GLN 0 195 " --> pdb=" O ARG 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 204 through 213 Processing helix chain '0' and resid 223 through 236 removed outlier: 3.977A pdb=" N LEU 0 227 " --> pdb=" O LEU 0 223 " (cutoff:3.500A) Processing helix chain '0' and resid 269 through 317 removed outlier: 4.689A pdb=" N GLY 0 280 " --> pdb=" O ARG 0 276 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU 0 283 " --> pdb=" O PHE 0 279 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG 0 286 " --> pdb=" O ALA 0 282 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE 0 297 " --> pdb=" O ASP 0 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 0 317 " --> pdb=" O GLU 0 313 " (cutoff:3.500A) Processing helix chain '0' and resid 321 through 335 removed outlier: 3.691A pdb=" N PHE 0 325 " --> pdb=" O ASN 0 321 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 413 Processing helix chain '0' and resid 415 through 429 removed outlier: 3.984A pdb=" N GLU 0 421 " --> pdb=" O ARG 0 417 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 0 424 " --> pdb=" O SER 0 420 " (cutoff:3.500A) Processing helix chain '0' and resid 456 through 458 No H-bonds generated for 'chain '0' and resid 456 through 458' Processing helix chain '0' and resid 466 through 477 Processing helix chain '0' and resid 503 through 517 removed outlier: 3.594A pdb=" N ALA 0 511 " --> pdb=" O ILE 0 507 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR 0 512 " --> pdb=" O MET 0 508 " (cutoff:3.500A) Processing helix chain '0' and resid 534 through 536 No H-bonds generated for 'chain '0' and resid 534 through 536' Processing helix chain '0' and resid 561 through 565 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 15 through 26 Processing helix chain '1' and resid 68 through 73 removed outlier: 4.216A pdb=" N ALA 1 73 " --> pdb=" O LYS 1 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.126A pdb=" N SER E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 71 Processing helix chain 'F' and resid 98 through 102 removed outlier: 3.676A pdb=" N ILE F 101 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 102 through 121 Processing helix chain 'G' and resid 135 through 146 removed outlier: 3.988A pdb=" N MET G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 183 through 189 Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'H' and resid 3 through 21 Proline residue: H 14 - end of helix Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 46 through 49 Processing helix chain 'H' and resid 50 through 61 removed outlier: 6.297A pdb=" N GLU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 59 through 82 removed outlier: 3.747A pdb=" N ALA I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG I 70 " --> pdb=" O HIS I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'K' and resid 20 through 30 removed outlier: 4.215A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.878A pdb=" N GLN K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 120 through 136 Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 56 through 65 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.780A pdb=" N THR L 77 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'N' and resid 25 through 39 removed outlier: 4.125A pdb=" N GLU N 32 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 97 through 110 removed outlier: 4.114A pdb=" N MET N 101 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 121 Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.900A pdb=" N LEU O 106 " --> pdb=" O ALA O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 56 through 61 Processing helix chain 'P' and resid 80 through 85 removed outlier: 3.654A pdb=" N GLY P 84 " --> pdb=" O LYS P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'Q' and resid 44 through 59 Processing helix chain 'Q' and resid 110 through 125 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.240A pdb=" N SER R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 66 Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 70 through 88 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'U' and resid 7 through 21 removed outlier: 4.067A pdb=" N ARG U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 31 through 73 removed outlier: 3.570A pdb=" N GLN U 38 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG U 55 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 102 through 117 removed outlier: 3.541A pdb=" N PHE U 106 " --> pdb=" O ASP U 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.767A pdb=" N ALA W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 43 through 62 Processing helix chain 'W' and resid 65 through 67 No H-bonds generated for 'chain 'W' and resid 65 through 67' Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 14 through 23 removed outlier: 3.565A pdb=" N GLU X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 48 Processing helix chain 'b' and resid 20 through 22 No H-bonds generated for 'chain 'b' and resid 20 through 22' Processing helix chain 'b' and resid 51 through 55 Processing helix chain 'c' and resid 2 through 8 Processing helix chain 'c' and resid 12 through 35 Processing helix chain 'c' and resid 40 through 65 removed outlier: 4.159A pdb=" N ARG c 44 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE c 57 " --> pdb=" O MET c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 40 through 51 Processing helix chain 'f' and resid 9 through 17 Processing helix chain 'h' and resid 8 through 16 Processing helix chain 'h' and resid 17 through 24 removed outlier: 3.626A pdb=" N SER h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 37 Processing helix chain 'i' and resid 7 through 14 Processing helix chain 'i' and resid 37 through 45 Processing helix chain 'i' and resid 51 through 59 Processing helix chain 'i' and resid 60 through 63 removed outlier: 3.867A pdb=" N ALA i 63 " --> pdb=" O GLN i 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 60 through 63' Processing helix chain 'j' and resid 29 through 32 Processing sheet with id=AA1, first strand: chain '0' and resid 23 through 31 removed outlier: 6.586A pdb=" N HIS 0 38 " --> pdb=" O THR 0 25 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE 0 27 " --> pdb=" O ILE 0 36 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE 0 36 " --> pdb=" O ILE 0 27 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN 0 29 " --> pdb=" O ASP 0 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP 0 34 " --> pdb=" O GLN 0 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 87 through 92 removed outlier: 5.393A pdb=" N ILE 0 88 " --> pdb=" O LYS 0 105 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS 0 105 " --> pdb=" O ILE 0 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE 0 129 " --> pdb=" O GLY 0 142 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY 0 142 " --> pdb=" O ILE 0 129 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU 0 131 " --> pdb=" O ILE 0 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 250 through 253 removed outlier: 3.651A pdb=" N TYR 0 253 " --> pdb=" O ASN 0 242 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 0 242 " --> pdb=" O TYR 0 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 345 through 349 Processing sheet with id=AA5, first strand: chain '0' and resid 451 through 454 removed outlier: 3.530A pdb=" N TYR 0 453 " --> pdb=" O ILE 0 461 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE 0 461 " --> pdb=" O TYR 0 453 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY 0 464 " --> pdb=" O HIS 0 494 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS 0 494 " --> pdb=" O GLY 0 464 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE 0 497 " --> pdb=" O ILE 0 483 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE 0 483 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 33 through 34 removed outlier: 6.796A pdb=" N LEU 1 55 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU 1 81 " --> pdb=" O LEU 1 55 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR 1 57 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 105 removed outlier: 6.612A pdb=" N ILE E 91 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU E 93 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 129 through 131 removed outlier: 6.702A pdb=" N LEU E 173 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS E 167 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 14 removed outlier: 5.390A pdb=" N LYS F 9 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU F 29 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY F 11 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU F 185 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 179 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU F 187 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU F 175 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL F 108 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL F 113 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 199 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.678A pdb=" N PHE F 79 " --> pdb=" O PHE F 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 48 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN F 37 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY F 52 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL F 35 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 116 through 120 Processing sheet with id=AB5, first strand: chain 'G' and resid 13 through 18 removed outlier: 5.661A pdb=" N GLY G 15 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 6 " --> pdb=" O GLY G 15 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N ILE G 123 " --> pdb=" O LYS G 3 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA G 5 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL G 125 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU G 153 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA G 152 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL G 176 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE G 154 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67 removed outlier: 6.840A pdb=" N VAL H 157 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE H 34 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL H 155 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE H 36 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP H 153 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AB8, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AB9, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AC1, first strand: chain 'I' and resid 96 through 98 Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.612A pdb=" N SER K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AC4, first strand: chain 'L' and resid 51 through 54 Processing sheet with id=AC5, first strand: chain 'N' and resid 123 through 125 removed outlier: 6.415A pdb=" N TRP N 16 " --> pdb=" O GLU N 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 74 through 78 Processing sheet with id=AC7, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.286A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA O 16 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA O 46 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU O 18 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL O 24 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL O 38 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA O 83 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N CYS O 84 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE O 86 " --> pdb=" O LYS O 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.720A pdb=" N THR T 58 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG T 50 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR T 60 " --> pdb=" O ILE T 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE T 64 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLU T 44 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP T 24 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR T 25 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS T 83 " --> pdb=" O HIS T 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS T 31 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE T 81 " --> pdb=" O LYS T 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 75 through 77 removed outlier: 6.052A pdb=" N ALA P 75 " --> pdb=" O LYS P 110 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL P 109 " --> pdb=" O LYS P 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 90 through 91 removed outlier: 6.304A pdb=" N VAL P 123 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.665A pdb=" N VAL Q 102 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA Q 36 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE Q 104 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 40 through 43 removed outlier: 5.392A pdb=" N ALA Q 76 " --> pdb=" O PRO Q 90 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY Q 92 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR Q 74 " --> pdb=" O GLY Q 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 29 through 33 removed outlier: 4.273A pdb=" N MET R 114 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 70 through 72 removed outlier: 3.702A pdb=" N ASN R 72 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.747A pdb=" N ILE S 44 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA S 42 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL S 33 " --> pdb=" O ASP S 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 11 through 14 Processing sheet with id=AD8, first strand: chain 'V' and resid 19 through 22 removed outlier: 3.572A pdb=" N LYS V 64 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR V 96 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL V 62 " --> pdb=" O THR V 96 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU V 98 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA V 60 " --> pdb=" O GLU V 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE V 100 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL V 58 " --> pdb=" O ILE V 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 71 through 75 Processing sheet with id=AE1, first strand: chain 'W' and resid 3 through 10 removed outlier: 6.337A pdb=" N SER W 101 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER W 108 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE W 71 " --> pdb=" O SER W 108 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 82 through 87 Processing sheet with id=AE3, first strand: chain 'X' and resid 8 through 10 removed outlier: 4.012A pdb=" N ARG X 77 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AE5, first strand: chain 'Y' and resid 23 through 27 removed outlier: 4.220A pdb=" N ALA Y 25 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 40 through 44 Processing sheet with id=AE7, first strand: chain 'Y' and resid 81 through 85 removed outlier: 3.949A pdb=" N GLN Y 99 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 30 through 31 removed outlier: 6.850A pdb=" N LEU a 67 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 38 through 39 Processing sheet with id=AF1, first strand: chain 'b' and resid 13 through 18 Processing sheet with id=AF2, first strand: chain 'b' and resid 33 through 36 Processing sheet with id=AF3, first strand: chain 'd' and resid 35 through 38 Processing sheet with id=AF4, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AF5, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'g' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'i' and resid 15 through 16 Processing sheet with id=AF8, first strand: chain 'j' and resid 2 through 3 removed outlier: 6.123A pdb=" N LYS j 2 " --> pdb=" O LYS j 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN j 34 " --> pdb=" O VAL j 25 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2599 hydrogen bonds 4236 hydrogen bond angles 0 basepair planarities 1019 basepair parallelities 1614 stacking parallelities Total time for adding SS restraints: 160.71 Time building geometry restraints manager: 46.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 18896 1.33 - 1.45: 41229 1.45 - 1.58: 35783 1.58 - 1.71: 5800 1.71 - 1.83: 188 Bond restraints: 101896 Sorted by residual: bond pdb=" CA LEU R 119 " pdb=" CB LEU R 119 " ideal model delta sigma weight residual 1.526 1.436 0.090 1.76e-02 3.23e+03 2.60e+01 bond pdb=" C1' U A 405 " pdb=" N1 U A 405 " ideal model delta sigma weight residual 1.480 1.545 -0.065 1.50e-02 4.44e+03 1.85e+01 bond pdb=" CA VAL 0 496 " pdb=" CB VAL 0 496 " ideal model delta sigma weight residual 1.553 1.529 0.024 7.40e-03 1.83e+04 1.02e+01 bond pdb=" CB THR O 6 " pdb=" CG2 THR O 6 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.39e+00 bond pdb=" CA THR a 51 " pdb=" CB THR a 51 " ideal model delta sigma weight residual 1.531 1.442 0.089 3.28e-02 9.30e+02 7.38e+00 ... (remaining 101891 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.64: 13551 104.64 - 112.43: 58306 112.43 - 120.21: 44104 120.21 - 127.99: 30732 127.99 - 135.77: 5690 Bond angle restraints: 152383 Sorted by residual: angle pdb=" N PRO 0 544 " pdb=" CA PRO 0 544 " pdb=" CB PRO 0 544 " ideal model delta sigma weight residual 103.35 110.43 -7.08 8.70e-01 1.32e+00 6.63e+01 angle pdb=" N PRO 0 448 " pdb=" CA PRO 0 448 " pdb=" CB PRO 0 448 " ideal model delta sigma weight residual 103.17 110.28 -7.11 8.90e-01 1.26e+00 6.38e+01 angle pdb=" N PRO 0 491 " pdb=" CA PRO 0 491 " pdb=" CB PRO 0 491 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.45e+01 angle pdb=" N PRO 0 527 " pdb=" CA PRO 0 527 " pdb=" CB PRO 0 527 " ideal model delta sigma weight residual 102.67 110.51 -7.84 1.09e+00 8.42e-01 5.18e+01 angle pdb=" N PRO 0 559 " pdb=" CA PRO 0 559 " pdb=" CB PRO 0 559 " ideal model delta sigma weight residual 103.25 110.16 -6.91 1.05e+00 9.07e-01 4.33e+01 ... (remaining 152378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 57479 35.88 - 71.77: 6943 71.77 - 107.65: 784 107.65 - 143.53: 37 143.53 - 179.42: 47 Dihedral angle restraints: 65290 sinusoidal: 54445 harmonic: 10845 Sorted by residual: dihedral pdb=" C5' U 2 7 " pdb=" C4' U 2 7 " pdb=" C3' U 2 7 " pdb=" O3' U 2 7 " ideal model delta sinusoidal sigma weight residual 147.00 72.61 74.39 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" CA ASN V 50 " pdb=" C ASN V 50 " pdb=" N PRO V 51 " pdb=" CA PRO V 51 " ideal model delta harmonic sigma weight residual 180.00 129.49 50.51 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" C4' U 2 7 " pdb=" C3' U 2 7 " pdb=" C2' U 2 7 " pdb=" C1' U 2 7 " ideal model delta sinusoidal sigma weight residual -35.00 34.35 -69.35 1 8.00e+00 1.56e-02 9.71e+01 ... (remaining 65287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 17888 0.088 - 0.176: 1471 0.176 - 0.264: 119 0.264 - 0.352: 7 0.352 - 0.440: 4 Chirality restraints: 19489 Sorted by residual: chirality pdb=" C1' G A1757 " pdb=" O4' G A1757 " pdb=" C2' G A1757 " pdb=" N9 G A1757 " both_signs ideal model delta sigma weight residual False 2.46 2.02 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C3' G A1828 " pdb=" C4' G A1828 " pdb=" O3' G A1828 " pdb=" C2' G A1828 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C3' U 2 7 " pdb=" C4' U 2 7 " pdb=" O3' U 2 7 " pdb=" C2' U 2 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 19486 not shown) Planarity restraints: 8152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1757 " -0.038 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 G A1757 " 0.060 2.00e-02 2.50e+03 pdb=" C8 G A1757 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A1757 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A1757 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A1757 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G A1757 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G A1757 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A1757 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G A1757 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1757 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G A1757 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 9 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ASN H 9 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN H 9 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS H 10 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1789 " -0.043 2.00e-02 2.50e+03 2.01e-02 1.11e+01 pdb=" N9 A A1789 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A A1789 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A1789 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A1789 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A A1789 " -0.012 2.00e-02 2.50e+03 pdb=" N6 A A1789 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A1789 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A1789 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A1789 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A A1789 " 0.004 2.00e-02 2.50e+03 ... (remaining 8149 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 891 2.54 - 3.13: 72420 3.13 - 3.72: 189112 3.72 - 4.31: 258264 4.31 - 4.90: 355978 Nonbonded interactions: 876665 Sorted by model distance: nonbonded pdb=" O2' G A 810 " pdb=" O5' A A 811 " model vdw 1.949 2.440 nonbonded pdb=" O2' U A1790 " pdb=" O4' A A1791 " model vdw 1.984 2.440 nonbonded pdb=" OG1 THR H 68 " pdb=" O ILE H 85 " model vdw 2.001 2.440 nonbonded pdb=" OP2 G A2806 " pdb=" O2' A A2810 " model vdw 2.016 2.440 nonbonded pdb=" O2' G A2009 " pdb=" OP2 U A2011 " model vdw 2.021 2.440 ... (remaining 876660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 18.580 Check model and map are aligned: 1.050 Set scattering table: 0.630 Process input model: 340.210 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.230 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:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 377.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 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 : 0.011 0.103 101896 Z= 0.672 Angle : 0.936 13.973 152383 Z= 0.483 Chirality : 0.054 0.440 19489 Planarity : 0.006 0.072 8152 Dihedral : 23.491 179.419 58296 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.68 % Favored : 91.16 % Rotamer: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.12), residues: 3734 helix: -1.75 (0.12), residues: 1135 sheet: -2.93 (0.16), residues: 711 loop : -2.82 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP U 61 HIS 0.031 0.003 HIS Q 13 PHE 0.046 0.003 PHE R 84 TYR 0.029 0.003 TYR I 95 ARG 0.016 0.002 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1192 time to evaluate : 4.047 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: 0 123 MET cc_start: 0.7748 (mmp) cc_final: 0.6181 (mmp) REVERT: 1 21 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8679 (tm-30) REVERT: 1 25 GLN cc_start: 0.8299 (mt0) cc_final: 0.8052 (mt0) REVERT: 1 33 ASN cc_start: 0.9377 (m-40) cc_final: 0.9110 (m110) REVERT: 1 48 THR cc_start: 0.9253 (m) cc_final: 0.8959 (t) REVERT: 1 55 LEU cc_start: 0.9007 (tt) cc_final: 0.8630 (tt) REVERT: E 30 GLU cc_start: 0.8496 (tp30) cc_final: 0.8188 (tp30) REVERT: E 38 HIS cc_start: 0.7812 (p-80) cc_final: 0.7611 (p90) REVERT: E 66 ASP cc_start: 0.8372 (t0) cc_final: 0.7977 (t0) REVERT: E 98 ASP cc_start: 0.8455 (p0) cc_final: 0.8162 (p0) REVERT: E 124 ILE cc_start: 0.8912 (pp) cc_final: 0.8660 (mt) REVERT: E 145 GLU cc_start: 0.8389 (pt0) cc_final: 0.8171 (pt0) REVERT: F 44 ASP cc_start: 0.8661 (m-30) cc_final: 0.8220 (m-30) REVERT: F 53 PHE cc_start: 0.8814 (t80) cc_final: 0.8392 (t80) REVERT: F 103 SER cc_start: 0.9261 (p) cc_final: 0.9058 (m) REVERT: F 197 LYS cc_start: 0.9346 (mttt) cc_final: 0.9140 (mtpp) REVERT: G 48 THR cc_start: 0.8196 (p) cc_final: 0.7707 (p) REVERT: G 194 ILE cc_start: 0.9368 (mt) cc_final: 0.9100 (mt) REVERT: H 20 PHE cc_start: 0.8601 (m-80) cc_final: 0.8202 (m-10) REVERT: H 22 TYR cc_start: 0.8973 (m-80) cc_final: 0.8507 (m-80) REVERT: H 23 ASP cc_start: 0.7804 (t0) cc_final: 0.7506 (t0) REVERT: H 24 SER cc_start: 0.8320 (p) cc_final: 0.7679 (t) REVERT: H 26 MET cc_start: 0.8726 (mmm) cc_final: 0.8474 (tpp) REVERT: H 27 GLN cc_start: 0.8921 (mt0) cc_final: 0.8458 (mp10) REVERT: H 91 LEU cc_start: 0.8759 (mt) cc_final: 0.8496 (mt) REVERT: I 59 GLN cc_start: 0.8235 (mp10) cc_final: 0.7675 (mp10) REVERT: I 128 SER cc_start: 0.9264 (t) cc_final: 0.9056 (p) REVERT: K 125 MET cc_start: 0.9222 (mtp) cc_final: 0.8941 (mtt) REVERT: K 127 MET cc_start: 0.8960 (mtp) cc_final: 0.7879 (mmm) REVERT: L 14 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.9145 (pm20) REVERT: L 75 PHE cc_start: 0.9227 (m-80) cc_final: 0.8655 (m-10) REVERT: N 44 THR cc_start: 0.8680 (p) cc_final: 0.8437 (p) REVERT: N 99 GLU cc_start: 0.8568 (mp0) cc_final: 0.8222 (mp0) REVERT: N 126 TYR cc_start: 0.8462 (m-80) cc_final: 0.8212 (m-80) REVERT: O 37 ASP cc_start: 0.8418 (m-30) cc_final: 0.8177 (m-30) REVERT: O 73 ASP cc_start: 0.8294 (p0) cc_final: 0.7993 (p0) REVERT: O 75 SER cc_start: 0.8967 (m) cc_final: 0.8643 (p) REVERT: P 17 ASN cc_start: 0.8975 (t0) cc_final: 0.8433 (t0) REVERT: Q 48 GLU cc_start: 0.8095 (pp20) cc_final: 0.7895 (pp20) REVERT: Q 85 SER cc_start: 0.9236 (m) cc_final: 0.8981 (t) REVERT: Q 116 GLU cc_start: 0.8245 (tp30) cc_final: 0.7653 (tp30) REVERT: R 23 ASP cc_start: 0.7768 (m-30) cc_final: 0.7269 (m-30) REVERT: R 45 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7374 (mm-30) REVERT: R 72 ASN cc_start: 0.9121 (t0) cc_final: 0.8606 (t0) REVERT: R 89 THR cc_start: 0.9054 (p) cc_final: 0.8796 (p) REVERT: S 2 ILE cc_start: 0.8817 (tp) cc_final: 0.8421 (tp) REVERT: S 80 LEU cc_start: 0.9430 (tt) cc_final: 0.9103 (tt) REVERT: S 111 ASP cc_start: 0.8943 (m-30) cc_final: 0.8650 (m-30) REVERT: T 8 ILE cc_start: 0.9048 (tp) cc_final: 0.8832 (pt) REVERT: T 31 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8439 (mtmm) REVERT: T 63 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8685 (ttpt) REVERT: T 80 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7759 (ttmm) REVERT: V 44 ASP cc_start: 0.8034 (t70) cc_final: 0.7603 (t0) REVERT: V 45 ASN cc_start: 0.9013 (p0) cc_final: 0.8538 (p0) REVERT: W 64 MET cc_start: 0.7560 (mtm) cc_final: 0.6951 (mtm) REVERT: W 68 ASN cc_start: 0.8836 (t0) cc_final: 0.8416 (t0) REVERT: X 22 THR cc_start: 0.9352 (p) cc_final: 0.8941 (p) REVERT: X 55 ASN cc_start: 0.8692 (m110) cc_final: 0.8434 (m-40) REVERT: Y 22 THR cc_start: 0.9061 (p) cc_final: 0.8839 (t) REVERT: Y 45 SER cc_start: 0.8637 (m) cc_final: 0.8229 (p) REVERT: Y 60 GLU cc_start: 0.8396 (mp0) cc_final: 0.6871 (mp0) REVERT: Y 72 ASP cc_start: 0.8667 (t0) cc_final: 0.8384 (t0) REVERT: a 64 ASP cc_start: 0.8297 (t0) cc_final: 0.7979 (OUTLIER) REVERT: a 78 GLU cc_start: 0.7466 (mp0) cc_final: 0.7258 (mp0) REVERT: a 86 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8180 (ttpp) REVERT: a 88 SER cc_start: 0.8599 (p) cc_final: 0.8128 (p) REVERT: c 19 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8926 (ptpp) REVERT: c 27 ASN cc_start: 0.9399 (m-40) cc_final: 0.9090 (m110) REVERT: c 28 LEU cc_start: 0.9525 (mm) cc_final: 0.9117 (mm) REVERT: c 42 ARG cc_start: 0.9091 (mmm160) cc_final: 0.8878 (mmp-170) REVERT: d 3 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8554 (mmtp) REVERT: d 10 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8183 (ttp80) REVERT: d 17 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7139 (tp30) REVERT: d 20 ARG cc_start: 0.8418 (ttm110) cc_final: 0.8064 (mtm-85) REVERT: d 40 ASN cc_start: 0.8554 (t0) cc_final: 0.8159 (t0) REVERT: f 36 MET cc_start: 0.8213 (mmm) cc_final: 0.7879 (mmm) REVERT: f 37 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8042 (tttm) REVERT: f 39 SER cc_start: 0.9547 (m) cc_final: 0.9011 (p) REVERT: h 9 ASN cc_start: 0.8647 (m-40) cc_final: 0.8432 (m110) REVERT: i 19 SER cc_start: 0.8745 (p) cc_final: 0.8380 (p) outliers start: 1 outliers final: 4 residues processed: 1193 average time/residue: 1.9285 time to fit residues: 3040.5400 Evaluate side-chains 820 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 816 time to evaluate : 4.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 112 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain c residue 7 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 563 optimal weight: 10.0000 chunk 505 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 341 optimal weight: 7.9990 chunk 270 optimal weight: 0.8980 chunk 522 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 317 optimal weight: 0.8980 chunk 389 optimal weight: 8.9990 chunk 605 optimal weight: 2.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 28 HIS 0 33 HIS 0 38 HIS 0 326 GLN 0 335 ASN ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 86 ASN E 199 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 50 GLN F 173 ASN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 ASN G 67 GLN H 9 ASN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN N 96 ASN P 27 ASN P 114 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN R 61 GLN R 77 GLN S 49 ASN T 29 HIS U 44 ASN U 52 GLN U 72 ASN U 108 GLN V 81 ASN W 95 GLN Y 2 HIS b 16 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 33 GLN g 4 ASN h 6 GLN h 8 ASN i 60 GLN i 64 ASN j 34 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 101896 Z= 0.188 Angle : 0.674 13.033 152383 Z= 0.341 Chirality : 0.037 0.556 19489 Planarity : 0.005 0.074 8152 Dihedral : 24.472 179.800 50836 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 3.72 % Allowed : 18.75 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.14 (0.13), residues: 3734 helix: -0.16 (0.15), residues: 1137 sheet: -1.76 (0.18), residues: 680 loop : -2.09 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 65 HIS 0.012 0.001 HIS Q 13 PHE 0.028 0.002 PHE H 114 TYR 0.030 0.002 TYR I 95 ARG 0.013 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1005 time to evaluate : 4.074 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: 0 11 MET cc_start: 0.9075 (mmm) cc_final: 0.8669 (mmp) REVERT: 0 76 CYS cc_start: 0.8041 (t) cc_final: 0.7090 (p) REVERT: 0 123 MET cc_start: 0.7187 (mmp) cc_final: 0.6382 (mmm) REVERT: 0 270 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8281 (mp) REVERT: 1 38 SER cc_start: 0.9560 (p) cc_final: 0.9072 (m) REVERT: 1 45 ASP cc_start: 0.8519 (m-30) cc_final: 0.8126 (m-30) REVERT: 1 48 THR cc_start: 0.9363 (m) cc_final: 0.9039 (t) REVERT: 1 60 VAL cc_start: 0.8688 (t) cc_final: 0.8412 (m) REVERT: E 38 HIS cc_start: 0.7784 (p-80) cc_final: 0.7571 (p90) REVERT: E 66 ASP cc_start: 0.8452 (t0) cc_final: 0.8189 (t0) REVERT: E 98 ASP cc_start: 0.8663 (p0) cc_final: 0.8350 (p0) REVERT: E 229 ASP cc_start: 0.8794 (m-30) cc_final: 0.8546 (m-30) REVERT: F 14 GLN cc_start: 0.8293 (mt0) cc_final: 0.8081 (mt0) REVERT: F 29 GLU cc_start: 0.7860 (pp20) cc_final: 0.7657 (pp20) REVERT: F 44 ASP cc_start: 0.8670 (m-30) cc_final: 0.8266 (m-30) REVERT: F 178 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8980 (tttp) REVERT: G 35 ASP cc_start: 0.8848 (m-30) cc_final: 0.8518 (m-30) REVERT: G 48 THR cc_start: 0.8553 (p) cc_final: 0.8081 (p) REVERT: H 27 GLN cc_start: 0.8877 (mt0) cc_final: 0.8546 (mp10) REVERT: H 59 PHE cc_start: 0.8503 (t80) cc_final: 0.7956 (t80) REVERT: H 72 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8969 (ttpp) REVERT: H 101 ASP cc_start: 0.8257 (m-30) cc_final: 0.7748 (m-30) REVERT: H 134 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: H 168 GLU cc_start: 0.8427 (pp20) cc_final: 0.8218 (tm-30) REVERT: I 129 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8250 (mm-40) REVERT: K 53 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8406 (tp) REVERT: K 80 LYS cc_start: 0.8808 (mttt) cc_final: 0.8590 (mtpp) REVERT: K 95 ASN cc_start: 0.9160 (t0) cc_final: 0.8269 (t0) REVERT: K 125 MET cc_start: 0.9267 (mtp) cc_final: 0.9051 (mtt) REVERT: L 59 MET cc_start: 0.8535 (mmm) cc_final: 0.8275 (mmm) REVERT: L 76 LEU cc_start: 0.9138 (mm) cc_final: 0.8794 (mt) REVERT: L 97 ASN cc_start: 0.9415 (t0) cc_final: 0.9158 (t0) REVERT: N 12 ILE cc_start: 0.8975 (mm) cc_final: 0.8733 (mp) REVERT: N 44 THR cc_start: 0.8821 (p) cc_final: 0.8595 (p) REVERT: N 75 TYR cc_start: 0.9382 (m-80) cc_final: 0.9120 (m-80) REVERT: N 97 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.7914 (p90) REVERT: N 103 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8163 (mt-10) REVERT: N 118 GLN cc_start: 0.9093 (tp40) cc_final: 0.8871 (mm-40) REVERT: O 4 GLN cc_start: 0.8448 (pt0) cc_final: 0.8138 (pt0) REVERT: O 5 GLU cc_start: 0.8331 (mp0) cc_final: 0.7779 (mp0) REVERT: O 8 LEU cc_start: 0.9375 (mt) cc_final: 0.9106 (mt) REVERT: O 45 GLN cc_start: 0.8305 (mm110) cc_final: 0.8054 (mm110) REVERT: O 73 ASP cc_start: 0.8226 (p0) cc_final: 0.7915 (p0) REVERT: O 99 PHE cc_start: 0.9070 (m-80) cc_final: 0.8863 (m-80) REVERT: P 94 GLU cc_start: 0.8707 (mp0) cc_final: 0.8266 (pm20) REVERT: P 126 ASN cc_start: 0.9354 (m110) cc_final: 0.9118 (m110) REVERT: R 23 ASP cc_start: 0.7663 (m-30) cc_final: 0.7399 (m-30) REVERT: R 28 GLU cc_start: 0.7992 (mp0) cc_final: 0.7562 (mp0) REVERT: R 29 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8200 (ttp80) REVERT: R 45 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7363 (mm-30) REVERT: R 72 ASN cc_start: 0.8861 (t0) cc_final: 0.8379 (t0) REVERT: R 82 LYS cc_start: 0.8954 (tttt) cc_final: 0.8734 (tttm) REVERT: R 92 GLU cc_start: 0.8351 (mp0) cc_final: 0.8040 (mp0) REVERT: S 12 LEU cc_start: 0.9568 (mt) cc_final: 0.9313 (mm) REVERT: S 60 ASP cc_start: 0.8136 (m-30) cc_final: 0.7828 (m-30) REVERT: S 111 ASP cc_start: 0.8913 (m-30) cc_final: 0.8650 (m-30) REVERT: T 31 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8673 (mtmm) REVERT: T 57 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: T 71 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: T 80 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7703 (ttmm) REVERT: T 83 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8741 (ttpp) REVERT: T 103 LEU cc_start: 0.9386 (mt) cc_final: 0.9161 (mp) REVERT: U 97 ASP cc_start: 0.8432 (t0) cc_final: 0.8229 (t0) REVERT: U 107 ASN cc_start: 0.8920 (m110) cc_final: 0.8573 (m-40) REVERT: V 2 TYR cc_start: 0.6603 (p90) cc_final: 0.5967 (p90) REVERT: V 13 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8916 (ttpp) REVERT: V 44 ASP cc_start: 0.7959 (t70) cc_final: 0.7679 (t0) REVERT: V 45 ASN cc_start: 0.8893 (p0) cc_final: 0.8625 (p0) REVERT: V 57 THR cc_start: 0.9090 (p) cc_final: 0.8885 (t) REVERT: W 11 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.9000 (mmm160) REVERT: W 33 VAL cc_start: 0.9368 (t) cc_final: 0.9150 (m) REVERT: W 100 THR cc_start: 0.9178 (m) cc_final: 0.8650 (p) REVERT: X 55 ASN cc_start: 0.9122 (m110) cc_final: 0.8694 (m-40) REVERT: Y 22 THR cc_start: 0.9049 (p) cc_final: 0.8296 (t) REVERT: Y 45 SER cc_start: 0.8925 (m) cc_final: 0.8585 (p) REVERT: Y 59 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8951 (pt0) REVERT: Y 60 GLU cc_start: 0.8294 (mp0) cc_final: 0.8055 (mp0) REVERT: Y 71 LEU cc_start: 0.9181 (mt) cc_final: 0.8948 (mt) REVERT: Y 72 ASP cc_start: 0.8703 (t0) cc_final: 0.8469 (t0) REVERT: Y 99 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7798 (tt0) REVERT: a 18 THR cc_start: 0.8882 (p) cc_final: 0.8619 (t) REVERT: a 35 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: a 76 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8636 (mmmm) REVERT: a 80 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8668 (m-10) REVERT: b 10 LYS cc_start: 0.8947 (mttm) cc_final: 0.8644 (mttm) REVERT: b 22 MET cc_start: 0.8450 (mmt) cc_final: 0.8221 (mmm) REVERT: b 37 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7211 (tmm160) REVERT: c 16 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8359 (pp30) REVERT: c 17 LYS cc_start: 0.9285 (mmmt) cc_final: 0.9003 (mtpp) REVERT: c 24 GLU cc_start: 0.8559 (tp30) cc_final: 0.8356 (tp30) REVERT: c 27 ASN cc_start: 0.9427 (m-40) cc_final: 0.9108 (m110) REVERT: c 42 ARG cc_start: 0.9031 (mmm160) cc_final: 0.8684 (mmp-170) REVERT: d 3 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8519 (mptt) REVERT: d 5 GLU cc_start: 0.7480 (mp0) cc_final: 0.7273 (mp0) REVERT: d 17 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7289 (tp30) REVERT: d 20 ARG cc_start: 0.8488 (ttm110) cc_final: 0.7995 (mtm-85) REVERT: f 39 SER cc_start: 0.9418 (m) cc_final: 0.8978 (p) outliers start: 115 outliers final: 34 residues processed: 1041 average time/residue: 1.7263 time to fit residues: 2456.8439 Evaluate side-chains 919 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 871 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 207 PHE Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 24 ASP Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain V residue 13 LYS Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 61 ASN Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain a residue 35 ASP Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain d residue 7 THR Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain f residue 29 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 504 optimal weight: 0.9990 chunk 412 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 606 optimal weight: 2.9990 chunk 655 optimal weight: 10.0000 chunk 540 optimal weight: 1.9990 chunk 601 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 199 GLN F 50 GLN F 173 ASN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN H 63 GLN I 20 ASN I 23 ASN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN R 77 GLN S 43 GLN ** S 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 HIS U 38 GLN U 44 ASN U 52 GLN U 72 ASN U 108 GLN U 116 GLN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 33 GLN g 25 ASN h 8 ASN h 9 ASN i 40 GLN i 60 GLN i 64 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 101896 Z= 0.209 Angle : 0.623 12.780 152383 Z= 0.320 Chirality : 0.036 0.537 19489 Planarity : 0.005 0.069 8152 Dihedral : 24.286 179.932 50827 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 4.75 % Allowed : 21.53 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.51 (0.13), residues: 3734 helix: 0.32 (0.15), residues: 1133 sheet: -1.22 (0.19), residues: 706 loop : -1.75 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 65 HIS 0.010 0.001 HIS S 103 PHE 0.021 0.002 PHE 0 231 TYR 0.019 0.002 TYR H 8 ARG 0.010 0.001 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1005 time to evaluate : 4.089 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: 0 11 MET cc_start: 0.8958 (mmm) cc_final: 0.8500 (mmp) REVERT: 0 123 MET cc_start: 0.7133 (mmp) cc_final: 0.6328 (mmm) REVERT: 0 270 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8653 (pt) REVERT: 0 374 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8915 (mp10) REVERT: 1 38 SER cc_start: 0.9623 (p) cc_final: 0.9161 (m) REVERT: 1 47 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9172 (mm) REVERT: 1 48 THR cc_start: 0.9285 (m) cc_final: 0.8993 (t) REVERT: E 38 HIS cc_start: 0.7977 (p-80) cc_final: 0.7771 (p90) REVERT: E 66 ASP cc_start: 0.8647 (t0) cc_final: 0.8400 (t0) REVERT: E 98 ASP cc_start: 0.8730 (p0) cc_final: 0.8398 (p0) REVERT: E 229 ASP cc_start: 0.8854 (m-30) cc_final: 0.8559 (m-30) REVERT: F 44 ASP cc_start: 0.8740 (m-30) cc_final: 0.8349 (m-30) REVERT: G 48 THR cc_start: 0.8977 (p) cc_final: 0.8567 (p) REVERT: H 22 TYR cc_start: 0.9146 (m-80) cc_final: 0.8780 (m-80) REVERT: H 27 GLN cc_start: 0.8917 (mt0) cc_final: 0.8606 (mp10) REVERT: H 32 GLU cc_start: 0.8492 (tt0) cc_final: 0.8139 (tp30) REVERT: H 101 ASP cc_start: 0.8609 (m-30) cc_final: 0.8372 (m-30) REVERT: I 39 HIS cc_start: 0.8689 (t-90) cc_final: 0.8378 (t-90) REVERT: I 129 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8271 (mm-40) REVERT: K 113 MET cc_start: 0.8208 (mmm) cc_final: 0.7977 (mmt) REVERT: L 39 THR cc_start: 0.9446 (m) cc_final: 0.9158 (p) REVERT: L 45 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8828 (mt) REVERT: L 59 MET cc_start: 0.8708 (mmm) cc_final: 0.8467 (mmm) REVERT: L 97 ASN cc_start: 0.9416 (t0) cc_final: 0.9090 (t0) REVERT: N 97 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.7965 (p90) REVERT: N 99 GLU cc_start: 0.8647 (mp0) cc_final: 0.8445 (mp0) REVERT: N 103 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8210 (mt-10) REVERT: N 118 GLN cc_start: 0.9228 (tp40) cc_final: 0.9003 (mm-40) REVERT: O 5 GLU cc_start: 0.8398 (mp0) cc_final: 0.7954 (mp0) REVERT: O 8 LEU cc_start: 0.9416 (mt) cc_final: 0.9203 (mt) REVERT: O 18 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7803 (tp30) REVERT: O 45 GLN cc_start: 0.8361 (mm110) cc_final: 0.8099 (mm110) REVERT: O 73 ASP cc_start: 0.8253 (p0) cc_final: 0.7955 (p0) REVERT: O 99 PHE cc_start: 0.9137 (m-80) cc_final: 0.8870 (m-80) REVERT: P 17 ASN cc_start: 0.9178 (t0) cc_final: 0.8926 (t0) REVERT: P 126 ASN cc_start: 0.9449 (m110) cc_final: 0.9210 (m110) REVERT: Q 48 GLU cc_start: 0.8187 (pp20) cc_final: 0.7878 (pp20) REVERT: Q 107 SER cc_start: 0.8605 (p) cc_final: 0.8207 (m) REVERT: Q 116 GLU cc_start: 0.8210 (tp30) cc_final: 0.7794 (tp30) REVERT: R 23 ASP cc_start: 0.7978 (m-30) cc_final: 0.7717 (m-30) REVERT: R 28 GLU cc_start: 0.8181 (mp0) cc_final: 0.7688 (mp0) REVERT: R 29 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8225 (ttp80) REVERT: R 45 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7619 (mm-30) REVERT: R 72 ASN cc_start: 0.8828 (t0) cc_final: 0.8409 (t0) REVERT: S 12 LEU cc_start: 0.9591 (mt) cc_final: 0.9358 (mm) REVERT: S 60 ASP cc_start: 0.8143 (m-30) cc_final: 0.7892 (m-30) REVERT: S 111 ASP cc_start: 0.8931 (m-30) cc_final: 0.8634 (m-30) REVERT: T 8 ILE cc_start: 0.9221 (tp) cc_final: 0.8890 (tp) REVERT: T 31 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8611 (mtmm) REVERT: T 57 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7937 (mm-30) REVERT: T 80 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7794 (ttmm) REVERT: T 83 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8853 (ttpp) REVERT: U 19 LYS cc_start: 0.8697 (tptt) cc_final: 0.8404 (mmtt) REVERT: U 107 ASN cc_start: 0.8867 (m110) cc_final: 0.8606 (m-40) REVERT: V 13 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8944 (ttpp) REVERT: V 15 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7741 (mm-30) REVERT: W 100 THR cc_start: 0.9129 (m) cc_final: 0.8619 (p) REVERT: X 55 ASN cc_start: 0.9208 (m110) cc_final: 0.8820 (m110) REVERT: X 65 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7692 (tmm-80) REVERT: Y 10 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7506 (tpt) REVERT: Y 20 GLN cc_start: 0.8683 (mt0) cc_final: 0.8451 (mm-40) REVERT: Y 40 MET cc_start: 0.8250 (mmm) cc_final: 0.7567 (mmm) REVERT: Y 45 SER cc_start: 0.9083 (m) cc_final: 0.8744 (p) REVERT: Y 60 GLU cc_start: 0.8379 (mp0) cc_final: 0.8133 (mp0) REVERT: Y 86 GLU cc_start: 0.7589 (pp20) cc_final: 0.7338 (pp20) REVERT: Y 89 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8506 (pmtt) REVERT: Y 99 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8018 (tt0) REVERT: a 35 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: a 80 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8537 (m-10) REVERT: a 86 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8462 (ttmt) REVERT: b 10 LYS cc_start: 0.9015 (mttm) cc_final: 0.8749 (mttm) REVERT: b 37 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7310 (tmm160) REVERT: c 1 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8082 (mmm) REVERT: c 17 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8858 (mtpp) REVERT: c 24 GLU cc_start: 0.8614 (tp30) cc_final: 0.8293 (tp30) REVERT: c 27 ASN cc_start: 0.9421 (m-40) cc_final: 0.9078 (m110) REVERT: d 3 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8433 (mmtt) REVERT: d 5 GLU cc_start: 0.7452 (mp0) cc_final: 0.7231 (mp0) REVERT: d 17 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7368 (tp30) REVERT: d 20 ARG cc_start: 0.8594 (ttm110) cc_final: 0.8107 (mtm-85) REVERT: f 39 SER cc_start: 0.9407 (m) cc_final: 0.8655 (p) REVERT: g 14 GLU cc_start: 0.7703 (tp30) cc_final: 0.7393 (tp30) REVERT: h 1 MET cc_start: 0.7205 (mtp) cc_final: 0.6808 (mtm) outliers start: 147 outliers final: 63 residues processed: 1054 average time/residue: 1.6283 time to fit residues: 2373.9748 Evaluate side-chains 970 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 891 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 207 PHE Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 285 ASP Chi-restraints excluded: chain 0 residue 374 GLN Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 71 GLU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 54 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 142 THR Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain V residue 13 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 108 SER Chi-restraints excluded: chain W residue 110 LYS Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 65 ARG Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 10 MET Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 35 ASP Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 23 GLU Chi-restraints excluded: chain d residue 7 THR Chi-restraints excluded: chain d residue 48 ASN Chi-restraints excluded: chain f residue 29 GLU Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain h residue 43 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 LYS Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 599 optimal weight: 2.9990 chunk 456 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 608 optimal weight: 0.7980 chunk 644 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 577 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 overall best weight: 6.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 HIS ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN P 38 GLN P 114 ASN Q 13 HIS R 12 GLN R 68 ASN R 77 GLN T 2 GLN U 38 GLN U 44 ASN U 52 GLN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN V 81 ASN Y 44 HIS h 9 ASN i 60 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 101896 Z= 0.365 Angle : 0.677 12.125 152383 Z= 0.351 Chirality : 0.040 0.540 19489 Planarity : 0.005 0.085 8152 Dihedral : 24.239 179.301 50827 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.59 % Favored : 93.36 % Rotamer: Outliers : 6.01 % Allowed : 24.60 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.27 (0.13), residues: 3734 helix: 0.42 (0.15), residues: 1125 sheet: -1.07 (0.18), residues: 749 loop : -1.53 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 250 HIS 0.011 0.002 HIS P 4 PHE 0.043 0.002 PHE 0 102 TYR 0.023 0.002 TYR S 102 ARG 0.009 0.001 ARG K 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 963 time to evaluate : 4.121 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: 0 11 MET cc_start: 0.8958 (mmm) cc_final: 0.8523 (mmp) REVERT: 0 123 MET cc_start: 0.7460 (mmp) cc_final: 0.6284 (mmm) REVERT: 0 270 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8760 (pt) REVERT: 1 9 VAL cc_start: 0.9063 (m) cc_final: 0.8859 (p) REVERT: 1 47 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9156 (tm) REVERT: 1 48 THR cc_start: 0.9169 (m) cc_final: 0.8858 (t) REVERT: E 30 GLU cc_start: 0.8694 (tp30) cc_final: 0.8310 (tp30) REVERT: E 66 ASP cc_start: 0.8802 (t0) cc_final: 0.8473 (t0) REVERT: E 98 ASP cc_start: 0.8894 (p0) cc_final: 0.8570 (p0) REVERT: E 145 GLU cc_start: 0.8237 (pt0) cc_final: 0.7983 (pt0) REVERT: E 225 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8661 (mmm) REVERT: F 26 THR cc_start: 0.9463 (m) cc_final: 0.9213 (m) REVERT: F 44 ASP cc_start: 0.8756 (m-30) cc_final: 0.8384 (m-30) REVERT: H 22 TYR cc_start: 0.9220 (m-80) cc_final: 0.8781 (m-80) REVERT: H 27 GLN cc_start: 0.9014 (mt0) cc_final: 0.8678 (mp10) REVERT: H 32 GLU cc_start: 0.8472 (tt0) cc_final: 0.8152 (tp30) REVERT: H 56 GLU cc_start: 0.9018 (pp20) cc_final: 0.8813 (pp20) REVERT: H 95 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8586 (ptt90) REVERT: H 97 TYR cc_start: 0.8400 (m-10) cc_final: 0.8147 (m-10) REVERT: H 134 GLU cc_start: 0.8148 (tp30) cc_final: 0.7923 (tp30) REVERT: I 41 ASP cc_start: 0.8507 (p0) cc_final: 0.8113 (p0) REVERT: I 45 LYS cc_start: 0.8451 (tmtt) cc_final: 0.8191 (tptt) REVERT: I 129 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8434 (mm-40) REVERT: K 102 ARG cc_start: 0.9506 (mmt90) cc_final: 0.9272 (mpt-90) REVERT: K 113 MET cc_start: 0.8380 (mmm) cc_final: 0.7642 (mmt) REVERT: K 125 MET cc_start: 0.8877 (mtt) cc_final: 0.8607 (mpt) REVERT: K 127 MET cc_start: 0.8991 (mtt) cc_final: 0.7908 (mmt) REVERT: K 137 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8333 (tt) REVERT: L 39 THR cc_start: 0.9483 (m) cc_final: 0.9212 (p) REVERT: L 45 LEU cc_start: 0.9060 (mt) cc_final: 0.8785 (mt) REVERT: L 61 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8575 (mtt90) REVERT: L 73 ASN cc_start: 0.8083 (m-40) cc_final: 0.7854 (m110) REVERT: L 97 ASN cc_start: 0.9486 (t0) cc_final: 0.9133 (t0) REVERT: N 38 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8594 (ttt90) REVERT: N 97 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7911 (p90) REVERT: N 99 GLU cc_start: 0.8748 (mp0) cc_final: 0.8474 (mp0) REVERT: N 103 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8260 (mt-10) REVERT: N 118 GLN cc_start: 0.9370 (tp40) cc_final: 0.9138 (mm-40) REVERT: O 5 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: O 18 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: O 44 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8604 (mmtm) REVERT: O 45 GLN cc_start: 0.8522 (mm110) cc_final: 0.8311 (mm110) REVERT: O 73 ASP cc_start: 0.8314 (p0) cc_final: 0.8103 (p0) REVERT: O 94 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8425 (ptm160) REVERT: P 17 ASN cc_start: 0.9294 (t0) cc_final: 0.8987 (t0) REVERT: P 126 ASN cc_start: 0.9530 (m110) cc_final: 0.9200 (m110) REVERT: Q 107 SER cc_start: 0.8700 (p) cc_final: 0.8461 (m) REVERT: R 28 GLU cc_start: 0.8215 (mp0) cc_final: 0.7746 (mp0) REVERT: R 29 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8375 (ttp80) REVERT: R 45 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7775 (mm-30) REVERT: R 69 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: R 72 ASN cc_start: 0.8871 (t0) cc_final: 0.8427 (t0) REVERT: S 60 ASP cc_start: 0.8277 (m-30) cc_final: 0.7969 (m-30) REVERT: T 31 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8653 (mtmm) REVERT: T 57 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: T 80 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8254 (ttmm) REVERT: T 103 LEU cc_start: 0.9397 (mp) cc_final: 0.8955 (mm) REVERT: U 55 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8229 (mtp180) REVERT: U 107 ASN cc_start: 0.8871 (m110) cc_final: 0.8593 (m-40) REVERT: V 44 ASP cc_start: 0.8195 (t0) cc_final: 0.7981 (t0) REVERT: W 28 GLN cc_start: 0.8934 (mp10) cc_final: 0.8319 (mp10) REVERT: W 31 GLU cc_start: 0.8046 (pt0) cc_final: 0.7790 (pt0) REVERT: W 68 ASN cc_start: 0.8558 (t0) cc_final: 0.8301 (t0) REVERT: W 100 THR cc_start: 0.9171 (m) cc_final: 0.8682 (p) REVERT: X 44 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8427 (mm-30) REVERT: X 55 ASN cc_start: 0.9388 (m110) cc_final: 0.9031 (m110) REVERT: Y 10 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7794 (tpt) REVERT: Y 40 MET cc_start: 0.8389 (mmm) cc_final: 0.7756 (mmm) REVERT: Y 45 SER cc_start: 0.9281 (m) cc_final: 0.8994 (p) REVERT: Y 60 GLU cc_start: 0.8589 (mp0) cc_final: 0.8250 (mp0) REVERT: Y 99 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8113 (tt0) REVERT: a 80 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: a 86 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8563 (ttmt) REVERT: b 10 LYS cc_start: 0.9080 (mttm) cc_final: 0.8774 (mttm) REVERT: b 22 MET cc_start: 0.8944 (mmm) cc_final: 0.8513 (mmm) REVERT: c 1 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7679 (tpp) REVERT: c 5 GLU cc_start: 0.8692 (mp0) cc_final: 0.8319 (mp0) REVERT: c 17 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8813 (mtpp) REVERT: c 24 GLU cc_start: 0.8595 (tp30) cc_final: 0.8325 (tp30) REVERT: c 27 ASN cc_start: 0.9398 (m-40) cc_final: 0.9031 (m110) REVERT: c 45 GLU cc_start: 0.8567 (pt0) cc_final: 0.8276 (pt0) REVERT: d 3 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8633 (mmtt) REVERT: d 5 GLU cc_start: 0.7647 (mp0) cc_final: 0.7246 (mp0) REVERT: d 17 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7649 (tp30) REVERT: d 20 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8035 (mtm-85) REVERT: f 39 SER cc_start: 0.9408 (m) cc_final: 0.8982 (p) REVERT: g 41 LYS cc_start: 0.9479 (mtmm) cc_final: 0.9187 (ptmm) REVERT: i 65 ILE cc_start: 0.8908 (mt) cc_final: 0.8657 (mp) outliers start: 186 outliers final: 94 residues processed: 1030 average time/residue: 1.6354 time to fit residues: 2335.0218 Evaluate side-chains 1015 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 903 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 54 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain R residue 77 GLN Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 108 SER Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 10 MET Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 79 ARG Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 23 GLU Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain d residue 48 ASN Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain h residue 43 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 536 optimal weight: 4.9990 chunk 365 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 480 optimal weight: 50.0000 chunk 266 optimal weight: 10.0000 chunk 550 optimal weight: 0.6980 chunk 445 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 329 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 289 GLN 0 307 ASN 1 74 ASN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 148 ASN R 27 ASN R 68 ASN S 43 GLN T 41 GLN U 52 GLN U 72 ASN U 108 GLN V 81 ASN Y 58 ASN a 58 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 101896 Z= 0.274 Angle : 0.635 12.383 152383 Z= 0.329 Chirality : 0.037 0.531 19489 Planarity : 0.005 0.070 8152 Dihedral : 24.242 179.778 50827 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.55 % Rotamer: Outliers : 5.56 % Allowed : 26.83 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.12 (0.13), residues: 3734 helix: 0.51 (0.15), residues: 1126 sheet: -0.82 (0.19), residues: 742 loop : -1.50 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 65 HIS 0.010 0.001 HIS d 52 PHE 0.025 0.002 PHE F 53 TYR 0.026 0.002 TYR I 95 ARG 0.009 0.001 ARG g 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 990 time to evaluate : 4.099 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: 0 11 MET cc_start: 0.8924 (mmm) cc_final: 0.8548 (mmp) REVERT: 1 3 LEU cc_start: 0.9514 (tp) cc_final: 0.9274 (tt) REVERT: 1 28 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8991 (mp) REVERT: 1 47 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8967 (tm) REVERT: 1 50 ARG cc_start: 0.9001 (mtp-110) cc_final: 0.8418 (tpp80) REVERT: E 30 GLU cc_start: 0.8672 (tp30) cc_final: 0.8288 (tp30) REVERT: E 66 ASP cc_start: 0.8797 (t0) cc_final: 0.8432 (t0) REVERT: E 225 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8679 (mmm) REVERT: F 26 THR cc_start: 0.9473 (m) cc_final: 0.9244 (m) REVERT: F 44 ASP cc_start: 0.8799 (m-30) cc_final: 0.8432 (m-30) REVERT: F 120 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8568 (mm110) REVERT: G 156 THR cc_start: 0.9353 (p) cc_final: 0.9072 (t) REVERT: H 22 TYR cc_start: 0.9211 (m-80) cc_final: 0.8968 (m-80) REVERT: H 27 GLN cc_start: 0.8935 (mt0) cc_final: 0.8617 (mp10) REVERT: H 32 GLU cc_start: 0.8504 (tt0) cc_final: 0.8107 (tp30) REVERT: H 57 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9138 (mm) REVERT: H 94 GLU cc_start: 0.8993 (pm20) cc_final: 0.7410 (pm20) REVERT: H 95 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7857 (pmm-80) REVERT: I 129 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8594 (mm-40) REVERT: K 113 MET cc_start: 0.8460 (mmm) cc_final: 0.7803 (mmm) REVERT: K 127 MET cc_start: 0.8932 (mtt) cc_final: 0.7944 (mmm) REVERT: K 137 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8361 (tt) REVERT: L 13 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8814 (pp20) REVERT: L 39 THR cc_start: 0.9484 (m) cc_final: 0.9200 (p) REVERT: L 45 LEU cc_start: 0.9105 (mt) cc_final: 0.8850 (mt) REVERT: L 73 ASN cc_start: 0.8063 (m-40) cc_final: 0.7743 (m-40) REVERT: L 76 LEU cc_start: 0.9131 (mm) cc_final: 0.8787 (mt) REVERT: L 97 ASN cc_start: 0.9485 (t0) cc_final: 0.9117 (t0) REVERT: N 92 GLU cc_start: 0.8095 (pm20) cc_final: 0.7894 (pm20) REVERT: N 97 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7971 (p90) REVERT: N 99 GLU cc_start: 0.8727 (mp0) cc_final: 0.8364 (mp0) REVERT: N 103 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8247 (mt-10) REVERT: N 118 GLN cc_start: 0.9355 (tp40) cc_final: 0.9149 (mm-40) REVERT: O 5 GLU cc_start: 0.8377 (mp0) cc_final: 0.7980 (mp0) REVERT: O 18 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: O 53 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8962 (mmtp) REVERT: O 94 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8519 (ptm160) REVERT: P 17 ASN cc_start: 0.9304 (t0) cc_final: 0.9031 (t0) REVERT: P 95 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8459 (tp) REVERT: P 126 ASN cc_start: 0.9546 (m110) cc_final: 0.9241 (m110) REVERT: Q 107 SER cc_start: 0.8672 (p) cc_final: 0.8469 (m) REVERT: R 23 ASP cc_start: 0.8245 (m-30) cc_final: 0.7987 (m-30) REVERT: R 27 ASN cc_start: 0.9276 (m-40) cc_final: 0.9066 (m110) REVERT: R 28 GLU cc_start: 0.8190 (mp0) cc_final: 0.7774 (mp0) REVERT: R 29 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8375 (ttp80) REVERT: R 45 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7750 (mm-30) REVERT: R 69 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: R 72 ASN cc_start: 0.8958 (t0) cc_final: 0.8571 (t0) REVERT: S 12 LEU cc_start: 0.9544 (mm) cc_final: 0.9252 (mm) REVERT: S 60 ASP cc_start: 0.8227 (m-30) cc_final: 0.7893 (m-30) REVERT: T 40 ILE cc_start: 0.9307 (pp) cc_final: 0.9041 (mp) REVERT: T 57 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: T 85 GLU cc_start: 0.8708 (pt0) cc_final: 0.8434 (pt0) REVERT: U 107 ASN cc_start: 0.8922 (m110) cc_final: 0.8669 (m-40) REVERT: V 13 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8906 (ttpp) REVERT: W 31 GLU cc_start: 0.8021 (pt0) cc_final: 0.7795 (pt0) REVERT: W 67 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8709 (p0) REVERT: W 68 ASN cc_start: 0.8764 (t0) cc_final: 0.8329 (t0) REVERT: W 100 THR cc_start: 0.9157 (m) cc_final: 0.8662 (p) REVERT: X 16 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7691 (tpp-160) REVERT: X 44 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8327 (mm-30) REVERT: X 55 ASN cc_start: 0.9372 (m110) cc_final: 0.9020 (m110) REVERT: X 68 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.8269 (mtm-85) REVERT: Y 20 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: Y 40 MET cc_start: 0.8473 (mmm) cc_final: 0.8247 (mmm) REVERT: Y 45 SER cc_start: 0.9315 (m) cc_final: 0.9054 (p) REVERT: Y 59 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8980 (pt0) REVERT: Y 89 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8509 (pmtt) REVERT: a 49 ARG cc_start: 0.8794 (mmp80) cc_final: 0.8366 (mmp80) REVERT: a 64 ASP cc_start: 0.8225 (t0) cc_final: 0.7643 (t0) REVERT: a 80 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8518 (m-10) REVERT: a 86 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8860 (ttmt) REVERT: b 10 LYS cc_start: 0.9084 (mttm) cc_final: 0.8774 (mttm) REVERT: c 17 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8741 (mtpp) REVERT: c 27 ASN cc_start: 0.9392 (m-40) cc_final: 0.8990 (m110) REVERT: c 45 GLU cc_start: 0.8552 (pt0) cc_final: 0.8234 (pt0) REVERT: d 3 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8630 (mmtt) REVERT: d 5 GLU cc_start: 0.7610 (mp0) cc_final: 0.7167 (mp0) REVERT: f 39 SER cc_start: 0.9439 (m) cc_final: 0.8660 (p) REVERT: g 47 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7946 (tm-30) REVERT: g 48 THR cc_start: 0.8701 (p) cc_final: 0.8483 (p) REVERT: i 15 LYS cc_start: 0.7963 (tptt) cc_final: 0.7699 (ttmt) REVERT: i 65 ILE cc_start: 0.9020 (mt) cc_final: 0.8772 (mp) outliers start: 172 outliers final: 91 residues processed: 1056 average time/residue: 1.6105 time to fit residues: 2367.2861 Evaluate side-chains 1028 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 916 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 41 CYS Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 54 LYS Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 13 LYS Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 20 GLN Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 79 ARG Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain d residue 48 ASN Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain h residue 43 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 216 optimal weight: 10.0000 chunk 580 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 645 optimal weight: 9.9990 chunk 535 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN O 45 GLN R 68 ASN R 76 ASN S 43 GLN T 41 GLN U 44 ASN U 52 GLN U 107 ASN U 108 GLN V 81 ASN Y 39 ASN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 4 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 101896 Z= 0.438 Angle : 0.714 11.935 152383 Z= 0.371 Chirality : 0.042 0.526 19489 Planarity : 0.005 0.067 8152 Dihedral : 24.259 179.422 50825 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.88 % Rotamer: Outliers : 6.50 % Allowed : 28.12 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -1.07 (0.13), residues: 3734 helix: 0.50 (0.16), residues: 1125 sheet: -0.84 (0.19), residues: 737 loop : -1.41 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 65 HIS 0.015 0.002 HIS T 29 PHE 0.026 0.002 PHE F 53 TYR 0.026 0.002 TYR I 95 ARG 0.008 0.001 ARG h 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 932 time to evaluate : 4.076 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: 0 11 MET cc_start: 0.8950 (mmm) cc_final: 0.8519 (mmp) REVERT: 0 123 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6839 (mmt) REVERT: 0 270 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8805 (pt) REVERT: 0 374 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9115 (mp10) REVERT: 1 28 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9087 (mp) REVERT: 1 47 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8920 (tm) REVERT: E 66 ASP cc_start: 0.8888 (t0) cc_final: 0.8485 (t0) REVERT: E 225 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: F 44 ASP cc_start: 0.8796 (m-30) cc_final: 0.8420 (m-30) REVERT: G 156 THR cc_start: 0.9374 (p) cc_final: 0.9093 (t) REVERT: H 27 GLN cc_start: 0.8978 (mt0) cc_final: 0.8679 (mt0) REVERT: H 32 GLU cc_start: 0.8539 (tt0) cc_final: 0.8236 (tp30) REVERT: H 57 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9326 (mm) REVERT: H 95 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8718 (ptt90) REVERT: H 177 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: I 41 ASP cc_start: 0.8622 (p0) cc_final: 0.8407 (p0) REVERT: I 129 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8438 (mm-40) REVERT: K 36 MET cc_start: 0.8858 (pmm) cc_final: 0.8519 (tpt) REVERT: K 125 MET cc_start: 0.8509 (mpt) cc_final: 0.8302 (mpt) REVERT: K 127 MET cc_start: 0.9029 (mtt) cc_final: 0.7971 (mmm) REVERT: K 135 MET cc_start: 0.6910 (ptp) cc_final: 0.6350 (pmm) REVERT: L 39 THR cc_start: 0.9478 (m) cc_final: 0.9203 (p) REVERT: L 45 LEU cc_start: 0.9139 (mt) cc_final: 0.8882 (mt) REVERT: L 73 ASN cc_start: 0.7998 (m-40) cc_final: 0.7768 (m-40) REVERT: L 97 ASN cc_start: 0.9500 (t0) cc_final: 0.9132 (t0) REVERT: N 38 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.8599 (ttt90) REVERT: N 97 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.7887 (p90) REVERT: N 99 GLU cc_start: 0.8753 (mp0) cc_final: 0.8371 (mp0) REVERT: N 103 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8286 (mt-10) REVERT: O 5 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: O 18 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: O 53 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8993 (mmtp) REVERT: O 94 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8241 (ptm160) REVERT: P 17 ASN cc_start: 0.9346 (t0) cc_final: 0.9058 (t0) REVERT: P 126 ASN cc_start: 0.9535 (m110) cc_final: 0.9151 (m110) REVERT: Q 107 SER cc_start: 0.8781 (p) cc_final: 0.8544 (m) REVERT: R 28 GLU cc_start: 0.8231 (mp0) cc_final: 0.7784 (mp0) REVERT: R 29 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8369 (ttp80) REVERT: R 45 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7804 (mm-30) REVERT: R 69 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: R 72 ASN cc_start: 0.8966 (t0) cc_final: 0.8597 (t0) REVERT: R 76 ASN cc_start: 0.8668 (m-40) cc_final: 0.8365 (p0) REVERT: S 60 ASP cc_start: 0.8297 (m-30) cc_final: 0.7929 (m-30) REVERT: T 2 GLN cc_start: 0.8792 (pt0) cc_final: 0.8297 (pt0) REVERT: T 6 GLU cc_start: 0.8731 (mp0) cc_final: 0.8193 (mp0) REVERT: T 31 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8739 (mtmm) REVERT: T 85 GLU cc_start: 0.8694 (pt0) cc_final: 0.8444 (pt0) REVERT: V 13 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8940 (ttpp) REVERT: W 68 ASN cc_start: 0.8852 (t0) cc_final: 0.8608 (t0) REVERT: W 100 THR cc_start: 0.9218 (m) cc_final: 0.8678 (p) REVERT: X 16 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7741 (tpp-160) REVERT: X 44 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8245 (mm-30) REVERT: X 55 ASN cc_start: 0.9464 (m110) cc_final: 0.9114 (m110) REVERT: X 68 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8198 (mtm-85) REVERT: Y 39 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8829 (m110) REVERT: Y 45 SER cc_start: 0.9380 (m) cc_final: 0.9151 (p) REVERT: Y 59 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8914 (pt0) REVERT: Y 86 GLU cc_start: 0.7684 (pp20) cc_final: 0.7017 (pp20) REVERT: a 35 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: a 37 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.9028 (tt0) REVERT: a 49 ARG cc_start: 0.8897 (mmp80) cc_final: 0.8417 (mmp80) REVERT: a 64 ASP cc_start: 0.8295 (t0) cc_final: 0.7724 (t0) REVERT: a 80 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8435 (m-10) REVERT: a 86 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8515 (ttmt) REVERT: b 10 LYS cc_start: 0.9099 (mttm) cc_final: 0.8798 (mttm) REVERT: c 1 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: c 17 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8964 (mtpp) REVERT: c 27 ASN cc_start: 0.9351 (m-40) cc_final: 0.8975 (m110) REVERT: c 45 GLU cc_start: 0.8582 (pt0) cc_final: 0.8201 (pt0) REVERT: d 3 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8729 (mmtt) REVERT: d 5 GLU cc_start: 0.7571 (mp0) cc_final: 0.7102 (mp0) REVERT: f 39 SER cc_start: 0.9444 (m) cc_final: 0.8624 (p) REVERT: g 47 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8051 (tm-30) REVERT: i 15 LYS cc_start: 0.7940 (tptt) cc_final: 0.7690 (ttmt) REVERT: i 65 ILE cc_start: 0.9160 (mt) cc_final: 0.8911 (mp) outliers start: 201 outliers final: 119 residues processed: 1009 average time/residue: 1.5949 time to fit residues: 2249.8413 Evaluate side-chains 1060 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 915 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 374 GLN Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 77 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 42 PHE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 41 CYS Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 54 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 59 GLN Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 69 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain V residue 13 LYS Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 35 ASP Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 49 LYS Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain h residue 43 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 60 GLN Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 622 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 471 optimal weight: 5.9990 chunk 365 optimal weight: 0.9980 chunk 543 optimal weight: 10.0000 chunk 360 optimal weight: 0.0970 chunk 642 optimal weight: 0.9990 chunk 402 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 ASN E 199 GLN ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 ASN R 68 ASN S 43 GLN T 41 GLN U 52 GLN U 72 ASN U 107 ASN U 108 GLN Y 39 ASN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 4 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 101896 Z= 0.164 Angle : 0.620 13.847 152383 Z= 0.318 Chirality : 0.035 0.506 19489 Planarity : 0.004 0.065 8152 Dihedral : 24.250 179.399 50825 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 4.33 % Allowed : 30.74 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3734 helix: 0.57 (0.16), residues: 1128 sheet: -0.63 (0.19), residues: 731 loop : -1.35 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 65 HIS 0.011 0.001 HIS L 103 PHE 0.023 0.002 PHE K 68 TYR 0.020 0.001 TYR I 95 ARG 0.013 0.001 ARG 1 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1011 time to evaluate : 4.125 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: 0 11 MET cc_start: 0.8890 (mmm) cc_final: 0.8463 (mmp) REVERT: 0 100 MET cc_start: 0.8912 (ppp) cc_final: 0.8648 (pmm) REVERT: 0 123 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6856 (mmp) REVERT: 0 270 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8765 (pt) REVERT: 1 28 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9119 (mp) REVERT: 1 38 SER cc_start: 0.9645 (p) cc_final: 0.9202 (m) REVERT: 1 47 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8935 (tm) REVERT: E 66 ASP cc_start: 0.8814 (t0) cc_final: 0.8451 (t0) REVERT: E 225 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8572 (mmm) REVERT: F 44 ASP cc_start: 0.8834 (m-30) cc_final: 0.8544 (m-30) REVERT: G 156 THR cc_start: 0.9418 (p) cc_final: 0.9073 (t) REVERT: G 200 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8807 (mm-30) REVERT: H 6 GLU cc_start: 0.8991 (pm20) cc_final: 0.8501 (pm20) REVERT: H 11 GLU cc_start: 0.8924 (mp0) cc_final: 0.8574 (mp0) REVERT: H 22 TYR cc_start: 0.9224 (m-80) cc_final: 0.9012 (m-80) REVERT: H 27 GLN cc_start: 0.8963 (mt0) cc_final: 0.8540 (mt0) REVERT: H 32 GLU cc_start: 0.8482 (tt0) cc_final: 0.8116 (tp30) REVERT: H 94 GLU cc_start: 0.8951 (pm20) cc_final: 0.7340 (pm20) REVERT: H 95 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7721 (pmm-80) REVERT: H 177 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: I 41 ASP cc_start: 0.8548 (p0) cc_final: 0.8308 (p0) REVERT: I 129 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8690 (mm-40) REVERT: K 36 MET cc_start: 0.8855 (pmm) cc_final: 0.8540 (tpt) REVERT: K 58 ILE cc_start: 0.7009 (mm) cc_final: 0.6706 (mp) REVERT: K 113 MET cc_start: 0.8307 (mmm) cc_final: 0.7646 (mmm) REVERT: K 126 ARG cc_start: 0.9366 (mtt90) cc_final: 0.9039 (ttm110) REVERT: K 127 MET cc_start: 0.8987 (mtt) cc_final: 0.7805 (mmm) REVERT: L 39 THR cc_start: 0.9422 (m) cc_final: 0.9108 (p) REVERT: L 61 ARG cc_start: 0.8818 (ptp90) cc_final: 0.8587 (ptp90) REVERT: L 73 ASN cc_start: 0.8022 (m-40) cc_final: 0.7629 (m-40) REVERT: L 97 ASN cc_start: 0.9507 (t0) cc_final: 0.9103 (t0) REVERT: N 38 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8555 (ttt90) REVERT: N 97 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7973 (p90) REVERT: N 99 GLU cc_start: 0.8644 (mp0) cc_final: 0.8242 (mp0) REVERT: N 103 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8242 (mt-10) REVERT: O 18 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: O 53 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9002 (mmtp) REVERT: O 94 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8402 (ptm160) REVERT: P 17 ASN cc_start: 0.9329 (t0) cc_final: 0.9072 (t0) REVERT: P 126 ASN cc_start: 0.9540 (m110) cc_final: 0.9232 (m110) REVERT: Q 107 SER cc_start: 0.8626 (p) cc_final: 0.8408 (m) REVERT: R 28 GLU cc_start: 0.8201 (mp0) cc_final: 0.7938 (mp0) REVERT: R 29 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8355 (ttp80) REVERT: R 45 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7658 (mm-30) REVERT: R 69 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7520 (mm-30) REVERT: R 72 ASN cc_start: 0.8955 (t0) cc_final: 0.8634 (t0) REVERT: R 76 ASN cc_start: 0.8575 (m-40) cc_final: 0.8347 (p0) REVERT: S 12 LEU cc_start: 0.9526 (mm) cc_final: 0.9250 (mm) REVERT: S 60 ASP cc_start: 0.8200 (m-30) cc_final: 0.7854 (m-30) REVERT: T 31 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8774 (mtmm) REVERT: T 80 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8193 (mttp) REVERT: T 83 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9137 (tmmt) REVERT: T 85 GLU cc_start: 0.8653 (pt0) cc_final: 0.8424 (pt0) REVERT: V 13 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8712 (ttpp) REVERT: W 68 ASN cc_start: 0.8834 (t0) cc_final: 0.8602 (t0) REVERT: W 100 THR cc_start: 0.9136 (m) cc_final: 0.8560 (p) REVERT: X 16 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7712 (tpp-160) REVERT: X 44 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8251 (mm-30) REVERT: X 46 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8936 (mp) REVERT: X 55 ASN cc_start: 0.9342 (m110) cc_final: 0.8991 (m110) REVERT: X 69 TYR cc_start: 0.9083 (m-80) cc_final: 0.8447 (m-80) REVERT: Y 40 MET cc_start: 0.8383 (mmm) cc_final: 0.7952 (mmm) REVERT: Y 72 ASP cc_start: 0.8760 (t70) cc_final: 0.8467 (t70) REVERT: a 64 ASP cc_start: 0.8148 (t0) cc_final: 0.7782 (t0) REVERT: a 86 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8954 (ttpp) REVERT: b 10 LYS cc_start: 0.9115 (mttm) cc_final: 0.8812 (mttm) REVERT: b 22 MET cc_start: 0.8613 (mmm) cc_final: 0.8380 (mmm) REVERT: c 1 MET cc_start: 0.8199 (mtp) cc_final: 0.7911 (mmm) REVERT: c 5 GLU cc_start: 0.8588 (mp0) cc_final: 0.8381 (mp0) REVERT: c 27 ASN cc_start: 0.9300 (m-40) cc_final: 0.8905 (m110) REVERT: c 36 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7851 (mp10) REVERT: c 45 GLU cc_start: 0.8662 (pt0) cc_final: 0.8377 (pt0) REVERT: c 58 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8201 (tpp80) REVERT: d 5 GLU cc_start: 0.7484 (mp0) cc_final: 0.7013 (mp0) REVERT: d 17 GLU cc_start: 0.8174 (tp30) cc_final: 0.7392 (tp30) REVERT: f 37 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8420 (ttpp) REVERT: f 39 SER cc_start: 0.9213 (m) cc_final: 0.8407 (p) REVERT: g 47 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8180 (tm-30) REVERT: h 1 MET cc_start: 0.7623 (mtp) cc_final: 0.7258 (mtm) REVERT: i 15 LYS cc_start: 0.8015 (tptt) cc_final: 0.7713 (ttmt) REVERT: i 65 ILE cc_start: 0.9141 (mt) cc_final: 0.8900 (mp) outliers start: 134 outliers final: 69 residues processed: 1057 average time/residue: 1.6521 time to fit residues: 2448.0512 Evaluate side-chains 1014 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 927 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 27 ARG Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 41 CYS Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 59 GLN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain V residue 13 LYS Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 79 ARG Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 383 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 408 optimal weight: 3.9990 chunk 437 optimal weight: 0.0020 chunk 317 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 505 optimal weight: 10.0000 overall best weight: 4.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 ASN ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 HIS H 172 GLN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN Q 35 GLN R 68 ASN S 43 GLN U 44 ASN U 52 GLN U 107 ASN U 108 GLN Y 39 ASN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 101896 Z= 0.291 Angle : 0.651 13.482 152383 Z= 0.336 Chirality : 0.038 0.499 19489 Planarity : 0.005 0.064 8152 Dihedral : 24.182 179.246 50825 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 4.56 % Allowed : 31.67 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3734 helix: 0.62 (0.16), residues: 1128 sheet: -0.61 (0.19), residues: 741 loop : -1.35 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 93 HIS 0.014 0.001 HIS L 103 PHE 0.025 0.002 PHE H 59 TYR 0.025 0.002 TYR S 100 ARG 0.013 0.001 ARG 1 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 942 time to evaluate : 4.034 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: 0 6 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8018 (pmm) REVERT: 0 11 MET cc_start: 0.8868 (mmm) cc_final: 0.8453 (mmp) REVERT: 0 100 MET cc_start: 0.8904 (ppp) cc_final: 0.8661 (pmm) REVERT: 0 123 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6513 (mmm) REVERT: 0 270 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8806 (pt) REVERT: 1 27 ARG cc_start: 0.8502 (mtm110) cc_final: 0.8286 (mtm110) REVERT: 1 28 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9228 (mp) REVERT: 1 47 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8931 (tm) REVERT: E 66 ASP cc_start: 0.8863 (t0) cc_final: 0.8447 (t0) REVERT: E 72 ASP cc_start: 0.8055 (m-30) cc_final: 0.7779 (m-30) REVERT: E 225 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8631 (mmm) REVERT: F 44 ASP cc_start: 0.8839 (m-30) cc_final: 0.8505 (m-30) REVERT: G 156 THR cc_start: 0.9527 (p) cc_final: 0.9255 (t) REVERT: H 27 GLN cc_start: 0.8978 (mt0) cc_final: 0.8588 (mt0) REVERT: H 32 GLU cc_start: 0.8446 (tt0) cc_final: 0.8092 (tp30) REVERT: H 38 MET cc_start: 0.8752 (mmm) cc_final: 0.8551 (mmm) REVERT: H 95 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8495 (tmm-80) REVERT: H 162 THR cc_start: 0.8900 (p) cc_final: 0.8674 (p) REVERT: I 129 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8656 (mm-40) REVERT: K 36 MET cc_start: 0.8886 (pmm) cc_final: 0.8484 (tpt) REVERT: K 58 ILE cc_start: 0.7154 (mm) cc_final: 0.6870 (mp) REVERT: K 127 MET cc_start: 0.8989 (mtt) cc_final: 0.7903 (mmm) REVERT: L 39 THR cc_start: 0.9447 (m) cc_final: 0.9153 (p) REVERT: L 45 LEU cc_start: 0.9161 (mt) cc_final: 0.8870 (mt) REVERT: L 66 GLN cc_start: 0.7578 (pp30) cc_final: 0.7355 (pp30) REVERT: L 97 ASN cc_start: 0.9492 (t0) cc_final: 0.9085 (t0) REVERT: N 38 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8510 (ttt90) REVERT: N 97 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.7923 (p90) REVERT: N 99 GLU cc_start: 0.8678 (mp0) cc_final: 0.8335 (mp0) REVERT: N 103 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8282 (mt-10) REVERT: O 18 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: O 53 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9022 (mmtm) REVERT: O 94 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8453 (ptm160) REVERT: P 17 ASN cc_start: 0.9361 (t0) cc_final: 0.9093 (t0) REVERT: P 126 ASN cc_start: 0.9556 (m110) cc_final: 0.9209 (m110) REVERT: P 134 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8255 (mp0) REVERT: R 28 GLU cc_start: 0.8406 (mp0) cc_final: 0.8108 (mp0) REVERT: R 29 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8381 (ttp80) REVERT: R 45 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7749 (mm-30) REVERT: R 69 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7522 (mm-30) REVERT: R 72 ASN cc_start: 0.9000 (t0) cc_final: 0.8596 (t0) REVERT: R 76 ASN cc_start: 0.8635 (m-40) cc_final: 0.8361 (p0) REVERT: S 12 LEU cc_start: 0.9541 (mm) cc_final: 0.9263 (mm) REVERT: S 60 ASP cc_start: 0.8243 (m-30) cc_final: 0.7887 (m-30) REVERT: T 31 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8634 (mtmm) REVERT: T 80 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8269 (ttmm) REVERT: T 85 GLU cc_start: 0.8626 (pt0) cc_final: 0.8408 (pt0) REVERT: W 28 GLN cc_start: 0.8825 (mp10) cc_final: 0.8267 (mp10) REVERT: W 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8600 (t0) REVERT: W 100 THR cc_start: 0.9162 (m) cc_final: 0.8592 (p) REVERT: X 16 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7737 (tpp-160) REVERT: X 44 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8290 (mm-30) REVERT: X 55 ASN cc_start: 0.9399 (m110) cc_final: 0.9079 (m-40) REVERT: Y 39 ASN cc_start: 0.8986 (m110) cc_final: 0.8695 (m-40) REVERT: Y 60 GLU cc_start: 0.8177 (mp0) cc_final: 0.7962 (mp0) REVERT: a 64 ASP cc_start: 0.8126 (t0) cc_final: 0.7826 (t0) REVERT: b 4 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8801 (ptmm) REVERT: b 10 LYS cc_start: 0.9129 (mttm) cc_final: 0.8789 (mttm) REVERT: b 22 MET cc_start: 0.8849 (mmm) cc_final: 0.8375 (mmm) REVERT: c 1 MET cc_start: 0.8196 (mtp) cc_final: 0.7579 (mmm) REVERT: c 5 GLU cc_start: 0.8689 (mp0) cc_final: 0.8219 (mp0) REVERT: c 24 GLU cc_start: 0.8882 (tp30) cc_final: 0.8570 (tp30) REVERT: c 27 ASN cc_start: 0.9319 (m-40) cc_final: 0.8931 (m110) REVERT: c 36 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7850 (mp10) REVERT: c 42 ARG cc_start: 0.9218 (mmm160) cc_final: 0.8767 (mmp-170) REVERT: c 45 GLU cc_start: 0.8632 (pt0) cc_final: 0.8130 (pt0) REVERT: d 5 GLU cc_start: 0.7513 (mp0) cc_final: 0.7037 (mp0) REVERT: f 39 SER cc_start: 0.9282 (m) cc_final: 0.8490 (p) REVERT: g 47 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8027 (tm-30) REVERT: h 1 MET cc_start: 0.7684 (mtp) cc_final: 0.7307 (mtm) REVERT: i 15 LYS cc_start: 0.8014 (tptt) cc_final: 0.7715 (ttmt) REVERT: i 65 ILE cc_start: 0.9234 (mt) cc_final: 0.8990 (mp) outliers start: 141 outliers final: 83 residues processed: 991 average time/residue: 1.5803 time to fit residues: 2186.0922 Evaluate side-chains 1012 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 915 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 MET Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 42 PHE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 18 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 41 CYS Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 54 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 59 GLN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 28 HIS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 79 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 584 optimal weight: 9.9990 chunk 615 optimal weight: 8.9990 chunk 561 optimal weight: 0.5980 chunk 599 optimal weight: 6.9990 chunk 360 optimal weight: 0.0020 chunk 260 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 541 optimal weight: 3.9990 chunk 566 optimal weight: 9.9990 chunk 596 optimal weight: 0.0770 overall best weight: 2.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 ASN ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN R 68 ASN S 43 GLN T 41 GLN U 52 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 101896 Z= 0.184 Angle : 0.633 14.254 152383 Z= 0.324 Chirality : 0.035 0.485 19489 Planarity : 0.005 0.065 8152 Dihedral : 24.212 179.581 50825 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 3.36 % Allowed : 33.16 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3734 helix: 0.55 (0.16), residues: 1128 sheet: -0.58 (0.19), residues: 744 loop : -1.33 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 93 HIS 0.010 0.001 HIS T 29 PHE 0.033 0.002 PHE H 114 TYR 0.025 0.001 TYR I 95 ARG 0.011 0.001 ARG g 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 945 time to evaluate : 4.200 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: 0 6 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7988 (pmm) REVERT: 0 11 MET cc_start: 0.8848 (mmm) cc_final: 0.8443 (mmp) REVERT: 0 100 MET cc_start: 0.8905 (ppp) cc_final: 0.8646 (pmm) REVERT: 0 123 MET cc_start: 0.7642 (mmt) cc_final: 0.7417 (mmm) REVERT: 0 270 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8793 (pt) REVERT: 1 38 SER cc_start: 0.9656 (p) cc_final: 0.9201 (m) REVERT: 1 47 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8530 (tm) REVERT: 1 48 THR cc_start: 0.9155 (m) cc_final: 0.8647 (t) REVERT: E 66 ASP cc_start: 0.8837 (t0) cc_final: 0.8456 (t0) REVERT: E 225 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8596 (mmm) REVERT: F 44 ASP cc_start: 0.8857 (m-30) cc_final: 0.8552 (m-30) REVERT: G 156 THR cc_start: 0.9531 (p) cc_final: 0.9261 (t) REVERT: H 20 PHE cc_start: 0.8581 (m-10) cc_final: 0.8150 (m-10) REVERT: H 27 GLN cc_start: 0.8990 (mt0) cc_final: 0.8506 (mt0) REVERT: H 32 GLU cc_start: 0.8434 (tt0) cc_final: 0.8062 (tp30) REVERT: H 95 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8324 (tmm-80) REVERT: H 168 GLU cc_start: 0.9025 (pp20) cc_final: 0.8805 (pp20) REVERT: I 129 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8702 (mm-40) REVERT: K 36 MET cc_start: 0.8889 (pmm) cc_final: 0.8502 (tpt) REVERT: K 58 ILE cc_start: 0.7244 (mm) cc_final: 0.6978 (mp) REVERT: K 113 MET cc_start: 0.7944 (mmt) cc_final: 0.7183 (mmt) REVERT: K 127 MET cc_start: 0.8978 (mtt) cc_final: 0.7821 (mmt) REVERT: K 135 MET cc_start: 0.6744 (ptp) cc_final: 0.6208 (pmm) REVERT: L 39 THR cc_start: 0.9429 (m) cc_final: 0.9132 (p) REVERT: L 45 LEU cc_start: 0.9137 (mt) cc_final: 0.8859 (mt) REVERT: L 57 ASN cc_start: 0.6622 (m-40) cc_final: 0.5714 (m-40) REVERT: L 97 ASN cc_start: 0.9494 (t0) cc_final: 0.9067 (t0) REVERT: N 38 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8533 (ttt90) REVERT: N 97 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7872 (p90) REVERT: N 99 GLU cc_start: 0.8618 (mp0) cc_final: 0.8281 (mp0) REVERT: N 103 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8241 (mt-10) REVERT: O 53 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9066 (mmtp) REVERT: O 94 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8479 (ptm160) REVERT: P 17 ASN cc_start: 0.9355 (t0) cc_final: 0.9100 (t0) REVERT: P 126 ASN cc_start: 0.9560 (m110) cc_final: 0.9242 (m110) REVERT: R 28 GLU cc_start: 0.8364 (mp0) cc_final: 0.8038 (mp0) REVERT: R 29 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8326 (ttp80) REVERT: R 45 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7676 (mm-30) REVERT: R 69 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7499 (mm-30) REVERT: R 72 ASN cc_start: 0.8966 (t0) cc_final: 0.8609 (t0) REVERT: R 76 ASN cc_start: 0.8575 (m-40) cc_final: 0.8314 (p0) REVERT: S 12 LEU cc_start: 0.9538 (mm) cc_final: 0.9255 (mm) REVERT: S 60 ASP cc_start: 0.8220 (m-30) cc_final: 0.7852 (m-30) REVERT: T 85 GLU cc_start: 0.8639 (pt0) cc_final: 0.8426 (pt0) REVERT: W 28 GLN cc_start: 0.8877 (mp10) cc_final: 0.8237 (mp10) REVERT: W 68 ASN cc_start: 0.8766 (t0) cc_final: 0.8561 (t0) REVERT: W 100 THR cc_start: 0.9129 (m) cc_final: 0.8540 (p) REVERT: X 16 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7737 (tpp-160) REVERT: X 44 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8272 (mm-30) REVERT: X 46 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8957 (mp) REVERT: X 55 ASN cc_start: 0.9362 (m110) cc_final: 0.9058 (m-40) REVERT: Y 39 ASN cc_start: 0.8971 (m110) cc_final: 0.8762 (m110) REVERT: Y 60 GLU cc_start: 0.8262 (mp0) cc_final: 0.8053 (mm-30) REVERT: a 64 ASP cc_start: 0.8087 (t0) cc_final: 0.7876 (t0) REVERT: a 90 TYR cc_start: 0.8809 (m-80) cc_final: 0.8562 (m-80) REVERT: b 4 LYS cc_start: 0.9121 (ptpp) cc_final: 0.8802 (ptmm) REVERT: b 10 LYS cc_start: 0.9133 (mttm) cc_final: 0.8793 (mttm) REVERT: b 22 MET cc_start: 0.8780 (mmm) cc_final: 0.8335 (mmm) REVERT: b 54 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9006 (mm) REVERT: c 1 MET cc_start: 0.8125 (mtp) cc_final: 0.7648 (mmm) REVERT: c 5 GLU cc_start: 0.8663 (mp0) cc_final: 0.8316 (mp0) REVERT: c 36 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7817 (mp10) REVERT: c 45 GLU cc_start: 0.8625 (pt0) cc_final: 0.8413 (pt0) REVERT: c 58 ARG cc_start: 0.9011 (mmm-85) cc_final: 0.8500 (tpp80) REVERT: d 5 GLU cc_start: 0.7482 (mp0) cc_final: 0.5867 (mp0) REVERT: f 39 SER cc_start: 0.9285 (m) cc_final: 0.8660 (p) REVERT: g 14 GLU cc_start: 0.7889 (tp30) cc_final: 0.7547 (tp30) REVERT: g 38 ARG cc_start: 0.8769 (mtm180) cc_final: 0.8268 (mtp-110) REVERT: g 47 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7979 (tm-30) REVERT: h 1 MET cc_start: 0.7660 (mtp) cc_final: 0.7306 (mtm) REVERT: i 15 LYS cc_start: 0.8040 (tptt) cc_final: 0.7745 (ttmt) REVERT: i 65 ILE cc_start: 0.9204 (mt) cc_final: 0.8960 (mp) outliers start: 104 outliers final: 74 residues processed: 983 average time/residue: 1.5745 time to fit residues: 2172.7382 Evaluate side-chains 1008 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 921 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 MET Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 118 LEU Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 27 ARG Chi-restraints excluded: chain 1 residue 47 LEU Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 77 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 59 GLN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 79 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 23 GLU Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 60 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 393 optimal weight: 2.9990 chunk 633 optimal weight: 0.8980 chunk 386 optimal weight: 0.0570 chunk 300 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 664 optimal weight: 6.9990 chunk 611 optimal weight: 7.9990 chunk 529 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 408 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 GLN ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN O 45 GLN R 68 ASN S 43 GLN T 41 GLN U 52 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 101896 Z= 0.176 Angle : 0.635 17.724 152383 Z= 0.324 Chirality : 0.035 0.474 19489 Planarity : 0.005 0.095 8152 Dihedral : 24.167 179.257 50825 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 3.14 % Allowed : 33.81 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3734 helix: 0.51 (0.16), residues: 1129 sheet: -0.52 (0.19), residues: 724 loop : -1.31 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 93 HIS 0.008 0.001 HIS T 29 PHE 0.030 0.002 PHE H 59 TYR 0.028 0.001 TYR S 100 ARG 0.020 0.001 ARG c 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 946 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 6 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8030 (pmm) REVERT: 0 11 MET cc_start: 0.8843 (mmm) cc_final: 0.8505 (mmp) REVERT: 0 100 MET cc_start: 0.8915 (ppp) cc_final: 0.8668 (pmm) REVERT: 0 123 MET cc_start: 0.7664 (mmt) cc_final: 0.7297 (mmp) REVERT: 0 270 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8491 (mp) REVERT: 1 15 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7647 (mmm-85) REVERT: 1 38 SER cc_start: 0.9643 (p) cc_final: 0.9207 (m) REVERT: 1 48 THR cc_start: 0.9138 (m) cc_final: 0.8912 (t) REVERT: E 66 ASP cc_start: 0.8840 (t0) cc_final: 0.8444 (t0) REVERT: E 225 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8570 (mmm) REVERT: F 44 ASP cc_start: 0.8855 (m-30) cc_final: 0.8561 (m-30) REVERT: G 156 THR cc_start: 0.9527 (p) cc_final: 0.9251 (t) REVERT: H 23 ASP cc_start: 0.7477 (t0) cc_final: 0.7001 (t0) REVERT: H 27 GLN cc_start: 0.8936 (mt0) cc_final: 0.8325 (mt0) REVERT: H 32 GLU cc_start: 0.8376 (tt0) cc_final: 0.8076 (tp30) REVERT: H 83 MET cc_start: 0.8471 (pmm) cc_final: 0.8226 (pmt) REVERT: H 95 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8329 (tmm-80) REVERT: H 168 GLU cc_start: 0.8926 (pp20) cc_final: 0.8684 (pp20) REVERT: I 129 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8704 (mm-40) REVERT: K 36 MET cc_start: 0.8888 (pmm) cc_final: 0.8509 (tpt) REVERT: K 58 ILE cc_start: 0.7361 (mm) cc_final: 0.7089 (mp) REVERT: K 127 MET cc_start: 0.8946 (mtt) cc_final: 0.7771 (mmm) REVERT: K 133 ARG cc_start: 0.9211 (mtp-110) cc_final: 0.8790 (tmm-80) REVERT: K 135 MET cc_start: 0.6831 (ptp) cc_final: 0.6451 (pmm) REVERT: L 39 THR cc_start: 0.9434 (m) cc_final: 0.9133 (p) REVERT: L 45 LEU cc_start: 0.9119 (mt) cc_final: 0.8830 (mt) REVERT: L 61 ARG cc_start: 0.8837 (mpt-90) cc_final: 0.8469 (mpt180) REVERT: L 76 LEU cc_start: 0.9176 (mm) cc_final: 0.8831 (mm) REVERT: L 97 ASN cc_start: 0.9503 (t0) cc_final: 0.9088 (t0) REVERT: N 38 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8546 (ttt90) REVERT: N 97 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7953 (p90) REVERT: N 99 GLU cc_start: 0.8633 (mp0) cc_final: 0.8300 (mp0) REVERT: N 103 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8253 (mt-10) REVERT: O 5 GLU cc_start: 0.8334 (mp0) cc_final: 0.7634 (mp0) REVERT: O 53 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9068 (mmtp) REVERT: O 94 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8541 (ptm160) REVERT: P 1 MET cc_start: 0.7894 (ttm) cc_final: 0.7633 (ttt) REVERT: P 17 ASN cc_start: 0.9369 (t0) cc_final: 0.9130 (t0) REVERT: P 126 ASN cc_start: 0.9555 (m110) cc_final: 0.9283 (m110) REVERT: R 28 GLU cc_start: 0.8289 (mp0) cc_final: 0.8009 (mp0) REVERT: R 29 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8340 (ttp80) REVERT: R 31 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7732 (pp20) REVERT: R 45 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7666 (mm-30) REVERT: R 69 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7497 (mm-30) REVERT: R 72 ASN cc_start: 0.8963 (t0) cc_final: 0.8657 (t0) REVERT: R 76 ASN cc_start: 0.8558 (m-40) cc_final: 0.8301 (p0) REVERT: S 12 LEU cc_start: 0.9522 (mm) cc_final: 0.9239 (mm) REVERT: S 60 ASP cc_start: 0.8162 (m-30) cc_final: 0.7788 (m-30) REVERT: T 65 SER cc_start: 0.9449 (t) cc_final: 0.9113 (t) REVERT: T 85 GLU cc_start: 0.8624 (pt0) cc_final: 0.8416 (pt0) REVERT: U 19 LYS cc_start: 0.8991 (tptt) cc_final: 0.8752 (tptt) REVERT: W 28 GLN cc_start: 0.8879 (mp10) cc_final: 0.8263 (mp10) REVERT: X 44 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8269 (mm-30) REVERT: X 46 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8968 (mp) REVERT: X 55 ASN cc_start: 0.9344 (m110) cc_final: 0.9003 (m110) REVERT: Y 39 ASN cc_start: 0.8982 (m110) cc_final: 0.8769 (m110) REVERT: a 80 PHE cc_start: 0.8886 (m-10) cc_final: 0.8602 (m-10) REVERT: a 90 TYR cc_start: 0.8865 (m-80) cc_final: 0.8591 (m-80) REVERT: b 4 LYS cc_start: 0.9080 (ptpp) cc_final: 0.8769 (ptmm) REVERT: b 10 LYS cc_start: 0.9127 (mttm) cc_final: 0.8772 (mttm) REVERT: b 22 MET cc_start: 0.8738 (mmm) cc_final: 0.8336 (mmm) REVERT: c 1 MET cc_start: 0.7975 (mtp) cc_final: 0.7690 (mmm) REVERT: c 5 GLU cc_start: 0.8643 (mp0) cc_final: 0.8368 (mp0) REVERT: c 22 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9082 (mmmm) REVERT: c 36 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7769 (mp10) REVERT: c 58 ARG cc_start: 0.9027 (mmm-85) cc_final: 0.8426 (tpp80) REVERT: d 5 GLU cc_start: 0.7952 (mp0) cc_final: 0.7496 (pm20) REVERT: d 29 LYS cc_start: 0.9353 (mttp) cc_final: 0.8686 (mtmt) REVERT: f 37 LYS cc_start: 0.8656 (tttm) cc_final: 0.8327 (ttpp) REVERT: f 39 SER cc_start: 0.9148 (m) cc_final: 0.8292 (p) REVERT: g 14 GLU cc_start: 0.7926 (tp30) cc_final: 0.7602 (tp30) REVERT: g 38 ARG cc_start: 0.8765 (mtm180) cc_final: 0.8268 (mtp-110) REVERT: g 47 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7976 (tm-30) REVERT: i 15 LYS cc_start: 0.8033 (tptt) cc_final: 0.7740 (ttmt) REVERT: i 65 ILE cc_start: 0.9228 (mt) cc_final: 0.8982 (mp) outliers start: 97 outliers final: 65 residues processed: 981 average time/residue: 1.6238 time to fit residues: 2221.7148 Evaluate side-chains 1005 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 929 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 MET Chi-restraints excluded: chain 0 residue 50 LEU Chi-restraints excluded: chain 0 residue 118 LEU Chi-restraints excluded: chain 0 residue 270 LEU Chi-restraints excluded: chain 0 residue 374 GLN Chi-restraints excluded: chain 0 residue 428 GLU Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 59 GLN Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 27 THR Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 79 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain h residue 13 SER Chi-restraints excluded: chain i residue 10 SER Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 420 optimal weight: 9.9990 chunk 563 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 487 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 529 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 289 GLN ** 0 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN O 45 GLN R 61 GLN R 68 ASN S 43 GLN T 41 GLN U 44 ASN U 52 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN V 81 ASN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.039924 restraints weight = 348571.437| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 1.58 r_work: 0.2477 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 101896 Z= 0.376 Angle : 0.702 13.468 152383 Z= 0.362 Chirality : 0.040 0.485 19489 Planarity : 0.005 0.063 8152 Dihedral : 24.157 179.169 50825 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 3.52 % Allowed : 33.81 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3734 helix: 0.49 (0.16), residues: 1119 sheet: -0.68 (0.19), residues: 733 loop : -1.30 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 83 HIS 0.014 0.002 HIS T 29 PHE 0.029 0.002 PHE H 59 TYR 0.037 0.002 TYR I 95 ARG 0.017 0.001 ARG H 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32537.98 seconds wall clock time: 567 minutes 24.53 seconds (34044.53 seconds total)