Starting phenix.real_space_refine on Wed Mar 20 01:08:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/03_2024/5ady_3133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/03_2024/5ady_3133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/03_2024/5ady_3133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/03_2024/5ady_3133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/03_2024/5ady_3133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ady_3133/03_2024/5ady_3133_updated.pdb" } resolution = 4.5 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 ------------------------------------------------------------------------------- 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= 0.040 sd= 0.416 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3021 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 49296 2.51 5 N 18113 2.21 5 O 26831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 97364 Number of models: 1 Model: "" Number of chains: 35 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain: "6" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3403 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "7" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1231 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2504 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 10, 'rna3p': 106} Chain: "B" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 263, 'rna2p_pyr': 138, 'rna3p_pur': 1411, 'rna3p_pyr': 1091} Link IDs: {'rna2p': 401, 'rna3p': 2501} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 37.53, per 1000 atoms: 0.39 Number of scatterers: 97364 At special positions: 0 Unit cell: (232.014, 201.701, 239.009, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 3021 15.00 Mg 1 11.99 O 26831 8.00 N 18113 7.00 C 49296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.34 Conformation dependent library (CDL) restraints added in 5.1 seconds 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 40 sheets defined 24.4% alpha, 8.3% beta 797 base pairs and 999 stacking pairs defined. Time for finding SS restraints: 48.00 Creating SS restraints... Processing helix chain '0' and resid 9 through 15 removed outlier: 4.094A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 removed outlier: 3.976A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 37 Processing helix chain '3' and resid 7 through 10 No H-bonds generated for 'chain '3' and resid 7 through 10' Processing helix chain '3' and resid 37 through 44 removed outlier: 3.638A pdb=" N LEU 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 60 Processing helix chain '4' and resid 31 through 33 No H-bonds generated for 'chain '4' and resid 31 through 33' Processing helix chain '5' and resid 7 through 11 Processing helix chain '5' and resid 23 through 28 Processing helix chain '5' and resid 82 through 84 No H-bonds generated for 'chain '5' and resid 82 through 84' Processing helix chain '5' and resid 86 through 90 Processing helix chain '5' and resid 151 through 156 Processing helix chain '5' and resid 182 through 197 Processing helix chain '6' and resid 28 through 37 Processing helix chain '6' and resid 60 through 73 Processing helix chain '6' and resid 86 through 95 removed outlier: 3.651A pdb=" N LEU 6 95 " --> pdb=" O ASN 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 113 Processing helix chain '6' and resid 118 through 145 removed outlier: 3.850A pdb=" N THR 6 134 " --> pdb=" O ARG 6 130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG 6 135 " --> pdb=" O HIS 6 131 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL 6 137 " --> pdb=" O ALA 6 133 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG 6 138 " --> pdb=" O THR 6 134 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY 6 139 " --> pdb=" O ARG 6 135 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP 6 140 " --> pdb=" O LEU 6 136 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR 6 141 " --> pdb=" O VAL 6 137 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS 6 142 " --> pdb=" O ARG 6 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU 6 143 " --> pdb=" O GLY 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 161 through 192 removed outlier: 4.044A pdb=" N ARG 6 180 " --> pdb=" O SER 6 176 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL 6 181 " --> pdb=" O ARG 6 177 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER 6 191 " --> pdb=" O GLN 6 187 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG 6 192 " --> pdb=" O GLY 6 188 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 218 Processing helix chain '6' and resid 261 through 267 Processing helix chain '6' and resid 270 through 276 removed outlier: 3.922A pdb=" N GLU 6 273 " --> pdb=" O THR 6 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG 6 275 " --> pdb=" O GLN 6 272 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN 6 276 " --> pdb=" O GLU 6 273 " (cutoff:3.500A) Processing helix chain '6' and resid 291 through 304 removed outlier: 3.754A pdb=" N VAL 6 301 " --> pdb=" O ALA 6 297 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU 6 304 " --> pdb=" O THR 6 300 " (cutoff:3.500A) Processing helix chain '6' and resid 350 through 360 Processing helix chain '6' and resid 377 through 386 Processing helix chain '6' and resid 396 through 398 No H-bonds generated for 'chain '6' and resid 396 through 398' Processing helix chain '6' and resid 408 through 417 Processing helix chain '7' and resid 4 through 20 Processing helix chain '7' and resid 34 through 43 Processing helix chain '7' and resid 63 through 66 Processing helix chain '7' and resid 98 through 101 No H-bonds generated for 'chain '7' and resid 98 through 101' Processing helix chain '7' and resid 127 through 131 Processing helix chain '7' and resid 136 through 139 No H-bonds generated for 'chain '7' and resid 136 through 139' Processing helix chain '7' and resid 150 through 153 No H-bonds generated for 'chain '7' and resid 150 through 153' Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 39 removed outlier: 4.078A pdb=" N VAL E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.509A pdb=" N LYS E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 141 removed outlier: 3.969A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.792A pdb=" N GLU E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.779A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.078A pdb=" N MET F 95 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE F 98 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 102 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.773A pdb=" N ALA F 167 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 168 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 60 through 79 Processing helix chain 'G' and resid 137 through 151 removed outlier: 4.156A pdb=" N GLY G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 25 No H-bonds generated for 'chain 'H' and resid 23 through 25' Processing helix chain 'H' and resid 44 through 54 removed outlier: 4.405A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'I' and resid 20 through 23 No H-bonds generated for 'chain 'I' and resid 20 through 23' Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'I' and resid 102 through 115 removed outlier: 5.683A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 129 through 135 removed outlier: 4.203A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 25 through 36 removed outlier: 3.561A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 108 removed outlier: 3.565A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA J 104 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY J 107 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 4.377A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 109 through 117 removed outlier: 3.656A pdb=" N ILE K 115 " --> pdb=" O MET K 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 116 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 84 removed outlier: 3.545A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.641A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'M' and resid 43 through 57 removed outlier: 4.274A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.528A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 removed outlier: 3.820A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 55 removed outlier: 5.418A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 61 through 66 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 85 through 87 No H-bonds generated for 'chain 'N' and resid 85 through 87' Processing helix chain 'O' and resid 5 through 21 removed outlier: 5.133A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'O' and resid 68 through 85 removed outlier: 4.409A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 111 Processing helix chain 'P' and resid 7 through 11 Processing helix chain 'P' and resid 99 through 101 No H-bonds generated for 'chain 'P' and resid 99 through 101' Processing helix chain 'Q' and resid 6 through 20 removed outlier: 4.028A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA Q 20 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.287A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 99 removed outlier: 4.037A pdb=" N ALA Q 95 " --> pdb=" O ARG Q 91 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE Q 97 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 91 through 99' Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.534A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 16 No H-bonds generated for 'chain 'S' and resid 14 through 16' Processing helix chain 'S' and resid 18 through 21 No H-bonds generated for 'chain 'S' and resid 18 through 21' Processing helix chain 'S' and resid 32 through 38 removed outlier: 4.150A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 59 removed outlier: 3.502A pdb=" N VAL S 45 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 5 through 7 No H-bonds generated for 'chain 'T' and resid 5 through 7' Processing helix chain 'T' and resid 22 through 25 No H-bonds generated for 'chain 'T' and resid 22 through 25' Processing helix chain 'T' and resid 40 through 49 removed outlier: 3.529A pdb=" N ALA T 45 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS T 49 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 23 removed outlier: 4.014A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 73 removed outlier: 6.196A pdb=" N ALA X 68 " --> pdb=" O ASP X 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 21 Processing helix chain 'Y' and resid 28 through 33 Processing helix chain 'Y' and resid 41 through 59 removed outlier: 3.763A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL Y 50 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 25 Processing helix chain 'Z' and resid 41 through 50 Processing sheet with id= A, first strand: chain '1' and resid 6 through 11 Processing sheet with id= B, first strand: chain '1' and resid 34 through 39 Processing sheet with id= C, first strand: chain '4' and resid 15 through 18 Processing sheet with id= D, first strand: chain '5' and resid 43 through 46 Processing sheet with id= E, first strand: chain '5' and resid 62 through 64 Processing sheet with id= F, first strand: chain '6' and resid 77 through 80 removed outlier: 7.305A pdb=" N GLU 6 40 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU 6 13 " --> pdb=" O GLU 6 40 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU 6 42 " --> pdb=" O LEU 6 13 " (cutoff:3.500A) removed outlier: 12.470A pdb=" N HIS 6 15 " --> pdb=" O LEU 6 42 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL 6 44 " --> pdb=" O HIS 6 15 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '6' and resid 200 through 203 removed outlier: 6.447A pdb=" N LEU 6 279 " --> pdb=" O SER 6 201 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL 6 203 " --> pdb=" O LEU 6 279 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU 6 281 " --> pdb=" O VAL 6 203 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '6' and resid 236 through 238 Processing sheet with id= I, first strand: chain '6' and resid 389 through 394 removed outlier: 6.104A pdb=" N GLN 6 403 " --> pdb=" O GLU 6 390 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU 6 392 " --> pdb=" O SER 6 401 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER 6 401 " --> pdb=" O GLU 6 392 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '7' and resid 23 through 25 Processing sheet with id= K, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.831A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 172 through 174 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= N, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.259A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.550A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 128 through 130 Processing sheet with id= Q, first strand: chain 'G' and resid 15 through 19 Processing sheet with id= R, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.555A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS G 114 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= T, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= U, first strand: chain 'I' and resid 9 through 13 Processing sheet with id= V, first strand: chain 'J' and resid 15 through 18 removed outlier: 7.068A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 74 through 76 Processing sheet with id= X, first strand: chain 'K' and resid 58 through 61 Processing sheet with id= Y, first strand: chain 'K' and resid 68 through 70 Processing sheet with id= Z, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.787A pdb=" N MET K 6 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL K 18 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS K 39 " --> pdb=" O ILE K 21 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 75 through 77 removed outlier: 4.053A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE L 77 " --> pdb=" O LYS L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'M' and resid 32 through 35 removed outlier: 3.598A pdb=" N VAL M 131 " --> pdb=" O GLY M 32 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.722A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 25 through 30 Processing sheet with id= AE, first strand: chain 'P' and resid 24 through 32 removed outlier: 3.654A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE P 42 " --> pdb=" O VAL P 27 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'P' and resid 60 through 63 Processing sheet with id= AG, first strand: chain 'R' and resid 71 through 73 Processing sheet with id= AH, first strand: chain 'S' and resid 73 through 77 Processing sheet with id= AI, first strand: chain 'S' and resid 82 through 86 Processing sheet with id= AJ, first strand: chain 'T' and resid 30 through 33 Processing sheet with id= AK, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AL, first strand: chain 'V' and resid 38 through 43 removed outlier: 6.817A pdb=" N ILE V 89 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TYR V 31 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE V 91 " --> pdb=" O TYR V 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 32 through 38 Processing sheet with id= AN, first strand: chain 'Z' and resid 34 through 38 698 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1910 hydrogen bonds 2782 hydrogen bond angles 0 basepair planarities 797 basepair parallelities 999 stacking parallelities Total time for adding SS restraints: 107.58 Time building geometry restraints manager: 60.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10775 1.32 - 1.44: 45652 1.44 - 1.57: 42916 1.57 - 1.69: 6044 1.69 - 1.82: 186 Bond restraints: 105573 Sorted by residual: bond pdb=" N3B GNP 6 527 " pdb=" PG GNP 6 527 " ideal model delta sigma weight residual 1.801 1.568 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" O3A GNP 6 527 " pdb=" PB GNP 6 527 " ideal model delta sigma weight residual 1.687 1.498 0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C SER C 271 " pdb=" N LYS C 272 " ideal model delta sigma weight residual 1.329 1.224 0.105 1.40e-02 5.10e+03 5.60e+01 bond pdb=" C ILE U 102 " pdb=" N LYS U 103 " ideal model delta sigma weight residual 1.329 1.225 0.104 1.40e-02 5.10e+03 5.47e+01 bond pdb=" C LEU T 93 " pdb=" N ASP T 94 " ideal model delta sigma weight residual 1.329 1.226 0.103 1.40e-02 5.10e+03 5.43e+01 ... (remaining 105568 not shown) Histogram of bond angle deviations from ideal: 95.84 - 104.48: 13048 104.48 - 113.12: 67353 113.12 - 121.75: 52393 121.75 - 130.39: 23322 130.39 - 139.03: 1425 Bond angle restraints: 157541 Sorted by residual: angle pdb=" C LEU 6 372 " pdb=" N PRO 6 373 " pdb=" CA PRO 6 373 " ideal model delta sigma weight residual 120.38 134.42 -14.04 1.03e+00 9.43e-01 1.86e+02 angle pdb=" N PHE J 4 " pdb=" CA PHE J 4 " pdb=" C PHE J 4 " ideal model delta sigma weight residual 111.71 98.72 12.99 1.34e+00 5.57e-01 9.40e+01 angle pdb=" C PHE V 26 " pdb=" N PRO V 27 " pdb=" CA PRO V 27 " ideal model delta sigma weight residual 119.78 129.18 -9.40 1.03e+00 9.43e-01 8.33e+01 angle pdb=" N GLY 3 52 " pdb=" CA GLY 3 52 " pdb=" C GLY 3 52 " ideal model delta sigma weight residual 115.66 101.64 14.02 1.56e+00 4.11e-01 8.08e+01 angle pdb=" N THR T 29 " pdb=" CA THR T 29 " pdb=" C THR T 29 " ideal model delta sigma weight residual 110.53 121.89 -11.36 1.32e+00 5.74e-01 7.40e+01 ... (remaining 157536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 58600 36.00 - 72.00: 7867 72.00 - 107.99: 947 107.99 - 143.99: 45 143.99 - 179.99: 48 Dihedral angle restraints: 67507 sinusoidal: 55599 harmonic: 11908 Sorted by residual: dihedral pdb=" C5' G B2252 " pdb=" C4' G B2252 " pdb=" C3' G B2252 " pdb=" O3' G B2252 " ideal model delta sinusoidal sigma weight residual 147.00 73.44 73.56 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C4' G B2252 " pdb=" C3' G B2252 " pdb=" C2' G B2252 " pdb=" C1' G B2252 " ideal model delta sinusoidal sigma weight residual -35.00 34.24 -69.24 1 8.00e+00 1.56e-02 9.68e+01 dihedral pdb=" C4' U B1779 " pdb=" C3' U B1779 " pdb=" C2' U B1779 " pdb=" C1' U B1779 " ideal model delta sinusoidal sigma weight residual -35.00 34.15 -69.15 1 8.00e+00 1.56e-02 9.66e+01 ... (remaining 67504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 18159 0.094 - 0.189: 1844 0.189 - 0.283: 105 0.283 - 0.378: 4 0.378 - 0.472: 3 Chirality restraints: 20115 Sorted by residual: chirality pdb=" CA GLN 6 20 " pdb=" N GLN 6 20 " pdb=" C GLN 6 20 " pdb=" CB GLN 6 20 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" C3' G B2252 " pdb=" C4' G B2252 " pdb=" O3' G B2252 " pdb=" C2' G B2252 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C3' U B1779 " pdb=" C4' U B1779 " pdb=" O3' U B1779 " pdb=" C2' U B1779 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 20112 not shown) Planarity restraints: 8752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE W 25 " -0.025 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE W 25 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE W 25 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE W 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE W 25 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE W 25 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE W 25 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 97 " 0.035 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR P 97 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR P 97 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR P 97 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 97 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR P 97 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR P 97 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR P 97 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B1395 " 0.032 2.00e-02 2.50e+03 1.80e-02 8.91e+00 pdb=" N9 A B1395 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B1395 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B1395 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B1395 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A B1395 " 0.020 2.00e-02 2.50e+03 pdb=" N6 A B1395 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B1395 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B1395 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B1395 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A B1395 " 0.001 2.00e-02 2.50e+03 ... (remaining 8749 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 134 2.09 - 2.79: 30201 2.79 - 3.50: 174023 3.50 - 4.20: 308728 4.20 - 4.90: 409968 Nonbonded interactions: 923054 Sorted by model distance: nonbonded pdb=" CG PRO H 32 " pdb=" CG TRP X 38 " model vdw 1.391 3.660 nonbonded pdb=" O ARG 5 134 " pdb=" N LEU 5 136 " model vdw 1.460 2.520 nonbonded pdb=" CG PRO H 32 " pdb=" CB TRP X 38 " model vdw 1.495 3.840 nonbonded pdb=" CG1 VAL 6 365 " pdb=" CZ ARG 6 405 " model vdw 1.539 3.690 nonbonded pdb=" O ALA 6 366 " pdb=" O GLN 6 367 " model vdw 1.581 3.040 ... (remaining 923049 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.090 Extract box with map and model: 9.930 Check model and map are aligned: 1.060 Set scattering table: 0.700 Process input model: 318.120 Find NCS groups from input model: 1.720 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 336.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 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 0.233 105573 Z= 0.672 Angle : 1.275 16.032 157541 Z= 0.734 Chirality : 0.057 0.472 20115 Planarity : 0.006 0.064 8752 Dihedral : 24.870 179.989 59829 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 57.89 Ramachandran Plot: Outliers : 6.67 % Allowed : 11.68 % Favored : 81.65 % Rotamer: Outliers : 0.21 % Allowed : 1.24 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.35 (0.12), residues: 4126 helix: -3.40 (0.10), residues: 988 sheet: -3.77 (0.17), residues: 524 loop : -1.37 (0.13), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP E 78 HIS 0.014 0.004 HIS 2 16 PHE 0.056 0.004 PHE W 25 TYR 0.051 0.004 TYR P 97 ARG 0.021 0.002 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1071 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 25 ASN cc_start: 0.7389 (t0) cc_final: 0.7123 (t0) REVERT: 5 8 MET cc_start: 0.0600 (mtp) cc_final: 0.0155 (mtm) REVERT: 5 12 ARG cc_start: 0.3891 (mtt180) cc_final: 0.3609 (mtt180) REVERT: 5 121 MET cc_start: 0.3167 (mtm) cc_final: 0.2740 (mmt) REVERT: 6 77 VAL cc_start: 0.7859 (p) cc_final: 0.7453 (t) REVERT: 6 181 VAL cc_start: 0.7234 (t) cc_final: 0.6845 (t) REVERT: 6 299 ASN cc_start: 0.6189 (m-40) cc_final: 0.5871 (t0) REVERT: 7 143 MET cc_start: 0.5587 (mmm) cc_final: 0.2048 (ptt) REVERT: C 43 ASN cc_start: 0.7989 (t0) cc_final: 0.7685 (t0) REVERT: C 82 TYR cc_start: 0.4846 (t80) cc_final: 0.4250 (t80) REVERT: E 60 TRP cc_start: 0.4881 (m100) cc_final: 0.4562 (m100) REVERT: E 196 VAL cc_start: 0.7730 (m) cc_final: 0.7405 (t) REVERT: G 113 ASP cc_start: 0.7369 (m-30) cc_final: 0.6356 (p0) REVERT: H 68 ARG cc_start: -0.0018 (OUTLIER) cc_final: -0.1753 (mtt180) REVERT: I 67 THR cc_start: 0.6008 (m) cc_final: 0.5652 (m) REVERT: I 135 MET cc_start: 0.5661 (mtp) cc_final: 0.5434 (mtt) REVERT: J 120 ARG cc_start: 0.7553 (ttt-90) cc_final: 0.6322 (mpt180) REVERT: K 38 ILE cc_start: 0.6686 (pt) cc_final: 0.6299 (pt) REVERT: M 31 PHE cc_start: 0.7661 (m-10) cc_final: 0.6954 (m-10) REVERT: M 104 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5575 (mt-10) REVERT: N 20 MET cc_start: 0.8090 (ttp) cc_final: 0.7872 (tpt) REVERT: N 39 PRO cc_start: 0.8679 (Cg_exo) cc_final: 0.7797 (Cg_endo) REVERT: O 18 LEU cc_start: 0.7915 (mt) cc_final: 0.7480 (mp) REVERT: P 1 SER cc_start: 0.7033 (t) cc_final: 0.6665 (t) REVERT: P 23 ASP cc_start: 0.5852 (m-30) cc_final: 0.5561 (m-30) REVERT: P 65 ASN cc_start: 0.7818 (m110) cc_final: 0.7527 (m-40) REVERT: S 109 ASP cc_start: 0.5716 (m-30) cc_final: 0.5415 (m-30) REVERT: V 47 VAL cc_start: 0.7794 (t) cc_final: 0.7556 (t) REVERT: V 77 VAL cc_start: 0.7921 (p) cc_final: 0.7526 (p) REVERT: Z 4 ILE cc_start: 0.7177 (pt) cc_final: 0.6099 (pt) outliers start: 7 outliers final: 3 residues processed: 1076 average time/residue: 1.0077 time to fit residues: 1781.7973 Evaluate side-chains 585 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 581 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 596 optimal weight: 6.9990 chunk 535 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 360 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 553 optimal weight: 0.0040 chunk 214 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 411 optimal weight: 9.9990 chunk 641 optimal weight: 8.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN 3 23 HIS 3 42 HIS ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN 6 43 GLN 6 82 HIS 6 146 GLN ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN 6 367 GLN ** 7 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 148 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 29 HIS ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN F 22 ASN G 115 GLN G 138 GLN H 18 GLN I 5 GLN I 18 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN N 62 ASN N 81 ASN P 11 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 11 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 28 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN V 51 GLN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 19 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 105573 Z= 0.254 Angle : 0.851 15.363 157541 Z= 0.428 Chirality : 0.042 0.365 20115 Planarity : 0.006 0.078 8752 Dihedral : 25.549 179.707 51730 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 1.70 % Allowed : 10.83 % Favored : 87.47 % Rotamer: Outliers : 0.38 % Allowed : 4.13 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.46 (0.12), residues: 4126 helix: -2.12 (0.14), residues: 1049 sheet: -3.26 (0.17), residues: 578 loop : -2.18 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP X 38 HIS 0.015 0.002 HIS Q 13 PHE 0.036 0.003 PHE 6 111 TYR 0.038 0.003 TYR 6 205 ARG 0.040 0.001 ARG G 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 852 time to evaluate : 4.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 25 ASN cc_start: 0.7807 (t0) cc_final: 0.7439 (t0) REVERT: 1 33 LEU cc_start: 0.6262 (tp) cc_final: 0.6027 (tp) REVERT: 2 31 LEU cc_start: 0.8078 (pp) cc_final: 0.7139 (mp) REVERT: 4 7 VAL cc_start: 0.6978 (t) cc_final: 0.6640 (t) REVERT: 6 113 GLN cc_start: 0.6317 (tp-100) cc_final: 0.6091 (tp-100) REVERT: 6 179 GLU cc_start: 0.6074 (mm-30) cc_final: 0.5784 (mm-30) REVERT: 6 226 ASP cc_start: 0.7105 (p0) cc_final: 0.6677 (p0) REVERT: 7 122 GLN cc_start: 0.5953 (tt0) cc_final: 0.5412 (pm20) REVERT: 7 143 MET cc_start: 0.5580 (mmm) cc_final: 0.2177 (ptt) REVERT: C 82 TYR cc_start: 0.4725 (t80) cc_final: 0.4171 (t80) REVERT: D 157 LYS cc_start: 0.7350 (mtpt) cc_final: 0.6469 (ttpt) REVERT: G 9 VAL cc_start: 0.6346 (t) cc_final: 0.6031 (t) REVERT: G 113 ASP cc_start: 0.7081 (m-30) cc_final: 0.6672 (p0) REVERT: H 12 LEU cc_start: 0.7242 (tp) cc_final: 0.6891 (tt) REVERT: H 44 ILE cc_start: 0.7625 (pt) cc_final: 0.7353 (pt) REVERT: H 101 ASP cc_start: 0.5386 (m-30) cc_final: 0.5072 (m-30) REVERT: I 86 LYS cc_start: 0.6843 (tptt) cc_final: 0.6070 (tppt) REVERT: J 86 GLN cc_start: 0.8729 (pm20) cc_final: 0.8334 (pm20) REVERT: J 93 ILE cc_start: 0.8642 (pt) cc_final: 0.8181 (mm) REVERT: J 120 ARG cc_start: 0.7483 (ttt-90) cc_final: 0.6211 (mpt180) REVERT: L 135 ILE cc_start: 0.7775 (pt) cc_final: 0.7294 (pt) REVERT: M 31 PHE cc_start: 0.7063 (m-10) cc_final: 0.6654 (m-10) REVERT: N 37 THR cc_start: 0.7246 (p) cc_final: 0.6925 (p) REVERT: O 45 SER cc_start: 0.8055 (m) cc_final: 0.7784 (p) REVERT: P 7 LEU cc_start: 0.7219 (mt) cc_final: 0.6248 (mt) REVERT: P 15 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7023 (t0) REVERT: Q 56 PHE cc_start: 0.7309 (m-10) cc_final: 0.6994 (m-10) REVERT: R 76 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7231 (mtmt) REVERT: S 77 ASP cc_start: 0.8629 (p0) cc_final: 0.7885 (p0) REVERT: T 8 LEU cc_start: 0.6408 (mp) cc_final: 0.5859 (mt) REVERT: V 2 PHE cc_start: 0.5034 (m-10) cc_final: 0.4810 (m-10) REVERT: V 40 ILE cc_start: 0.6928 (pt) cc_final: 0.6631 (pt) REVERT: V 77 VAL cc_start: 0.8128 (p) cc_final: 0.7541 (p) REVERT: W 18 LYS cc_start: 0.5677 (mtmt) cc_final: 0.5242 (mtmt) REVERT: W 69 GLU cc_start: 0.6046 (pm20) cc_final: 0.5673 (pm20) REVERT: X 58 ILE cc_start: 0.7970 (mt) cc_final: 0.7174 (mt) REVERT: Z 4 ILE cc_start: 0.7443 (pt) cc_final: 0.6951 (pt) REVERT: Z 20 LYS cc_start: 0.7537 (mtpt) cc_final: 0.6984 (ttmt) REVERT: Z 22 THR cc_start: 0.8469 (m) cc_final: 0.8235 (p) outliers start: 13 outliers final: 5 residues processed: 861 average time/residue: 0.9588 time to fit residues: 1394.2179 Evaluate side-chains 562 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 556 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 356 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 533 optimal weight: 40.0000 chunk 436 optimal weight: 30.0000 chunk 176 optimal weight: 20.0000 chunk 642 optimal weight: 0.4980 chunk 693 optimal weight: 6.9990 chunk 572 optimal weight: 30.0000 chunk 636 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 chunk 515 optimal weight: 50.0000 overall best weight: 11.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN 0 41 HIS ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 33 HIS ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN H 18 GLN I 18 ASN I 30 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN R 6 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 105573 Z= 0.431 Angle : 0.995 12.061 157541 Z= 0.495 Chirality : 0.049 0.367 20115 Planarity : 0.008 0.147 8752 Dihedral : 25.595 179.362 51730 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 39.90 Ramachandran Plot: Outliers : 1.43 % Allowed : 14.15 % Favored : 84.42 % Rotamer: Outliers : 0.41 % Allowed : 5.96 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -3.74 (0.11), residues: 4126 helix: -2.15 (0.13), residues: 1037 sheet: -3.17 (0.17), residues: 625 loop : -2.51 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.006 TRP 6 341 HIS 0.014 0.003 HIS T 70 PHE 0.031 0.004 PHE J 4 TYR 0.051 0.004 TYR 0 48 ARG 0.042 0.002 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 740 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 43 THR cc_start: 0.7238 (m) cc_final: 0.6608 (m) REVERT: 0 48 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: 1 25 ASN cc_start: 0.8605 (t0) cc_final: 0.8319 (t0) REVERT: 2 31 LEU cc_start: 0.8489 (pp) cc_final: 0.7538 (mp) REVERT: 3 62 PRO cc_start: 0.7856 (Cg_endo) cc_final: 0.7569 (Cg_exo) REVERT: 5 121 MET cc_start: 0.3514 (mmt) cc_final: 0.2609 (mmt) REVERT: 5 218 MET cc_start: 0.2161 (mtm) cc_final: 0.1839 (mtm) REVERT: 6 177 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7346 (mtt-85) REVERT: 7 122 GLN cc_start: 0.6544 (tt0) cc_final: 0.5801 (pm20) REVERT: C 51 ARG cc_start: 0.8240 (mtm110) cc_final: 0.8027 (mtp85) REVERT: C 82 TYR cc_start: 0.5386 (t80) cc_final: 0.5000 (t80) REVERT: C 224 MET cc_start: 0.8684 (mtm) cc_final: 0.8471 (ptp) REVERT: D 157 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7431 (ttpt) REVERT: G 154 GLU cc_start: 0.7879 (pp20) cc_final: 0.6228 (pt0) REVERT: H 7 ASP cc_start: 0.8701 (m-30) cc_final: 0.8445 (m-30) REVERT: H 12 LEU cc_start: 0.7597 (tp) cc_final: 0.7347 (tt) REVERT: H 101 ASP cc_start: 0.5955 (m-30) cc_final: 0.5486 (m-30) REVERT: I 86 LYS cc_start: 0.7009 (tptt) cc_final: 0.6727 (tptt) REVERT: J 30 THR cc_start: 0.7388 (p) cc_final: 0.7033 (p) REVERT: J 93 ILE cc_start: 0.8901 (pt) cc_final: 0.8314 (mm) REVERT: L 55 MET cc_start: 0.6966 (tpp) cc_final: 0.6474 (tpp) REVERT: L 135 ILE cc_start: 0.8430 (pt) cc_final: 0.8141 (pt) REVERT: M 1 MET cc_start: 0.7796 (mmt) cc_final: 0.7451 (mmt) REVERT: M 73 ILE cc_start: 0.7866 (mt) cc_final: 0.7610 (mt) REVERT: N 102 PHE cc_start: 0.6379 (m-10) cc_final: 0.5999 (m-10) REVERT: O 45 SER cc_start: 0.8057 (m) cc_final: 0.7805 (p) REVERT: P 14 GLN cc_start: 0.7249 (tm-30) cc_final: 0.7017 (tm-30) REVERT: S 77 ASP cc_start: 0.8355 (p0) cc_final: 0.7582 (p0) REVERT: S 78 GLU cc_start: 0.6836 (pt0) cc_final: 0.6499 (pt0) REVERT: T 8 LEU cc_start: 0.7470 (mp) cc_final: 0.6808 (mt) REVERT: V 40 ILE cc_start: 0.7536 (pt) cc_final: 0.7335 (pt) REVERT: V 76 ASP cc_start: 0.6733 (m-30) cc_final: 0.5594 (m-30) REVERT: V 89 ILE cc_start: 0.6979 (tt) cc_final: 0.6610 (tt) REVERT: W 10 ARG cc_start: 0.8402 (mpp80) cc_final: 0.7983 (mpp80) REVERT: W 18 LYS cc_start: 0.6690 (mtmt) cc_final: 0.5967 (mttt) REVERT: W 36 ILE cc_start: 0.8470 (mm) cc_final: 0.7865 (mm) REVERT: W 77 LYS cc_start: 0.8230 (mttt) cc_final: 0.7694 (mttm) REVERT: Y 13 GLU cc_start: 0.4772 (tt0) cc_final: 0.4447 (tt0) REVERT: Z 5 LYS cc_start: 0.6766 (ttpp) cc_final: 0.6459 (ttpp) REVERT: Z 20 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7216 (ttmt) outliers start: 14 outliers final: 3 residues processed: 752 average time/residue: 0.9605 time to fit residues: 1221.8094 Evaluate side-chains 552 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 548 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 634 optimal weight: 7.9990 chunk 482 optimal weight: 20.0000 chunk 333 optimal weight: 50.0000 chunk 71 optimal weight: 6.9990 chunk 306 optimal weight: 30.0000 chunk 431 optimal weight: 20.0000 chunk 644 optimal weight: 0.0470 chunk 682 optimal weight: 8.9990 chunk 336 optimal weight: 30.0000 chunk 610 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 overall best weight: 6.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 18 GLN H 33 GLN I 5 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS P 11 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 105573 Z= 0.249 Angle : 0.725 11.798 157541 Z= 0.369 Chirality : 0.039 0.363 20115 Planarity : 0.005 0.073 8752 Dihedral : 25.300 179.870 51730 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 27.15 Ramachandran Plot: Outliers : 1.31 % Allowed : 10.93 % Favored : 87.76 % Rotamer: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.46 (0.12), residues: 4126 helix: -1.63 (0.14), residues: 1043 sheet: -2.93 (0.17), residues: 642 loop : -2.49 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 247 HIS 0.014 0.002 HIS 6 82 PHE 0.028 0.003 PHE X 28 TYR 0.040 0.002 TYR 6 205 ARG 0.020 0.001 ARG X 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 748 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 25 ASN cc_start: 0.8491 (t0) cc_final: 0.8237 (t0) REVERT: 2 4 THR cc_start: 0.8511 (p) cc_final: 0.8183 (t) REVERT: 2 31 LEU cc_start: 0.8747 (pp) cc_final: 0.7810 (mp) REVERT: 3 62 PRO cc_start: 0.7794 (Cg_endo) cc_final: 0.7525 (Cg_exo) REVERT: 5 121 MET cc_start: 0.3937 (mmt) cc_final: -0.0583 (mtp) REVERT: 6 177 ARG cc_start: 0.7546 (mtt180) cc_final: 0.7335 (mtt-85) REVERT: C 82 TYR cc_start: 0.5745 (t80) cc_final: 0.5199 (t80) REVERT: D 146 ILE cc_start: 0.8468 (pt) cc_final: 0.8229 (pt) REVERT: D 165 MET cc_start: 0.7826 (tpp) cc_final: 0.7525 (tpp) REVERT: F 25 MET cc_start: 0.5738 (mmp) cc_final: 0.5110 (mmp) REVERT: G 9 VAL cc_start: 0.7042 (t) cc_final: 0.6791 (t) REVERT: G 31 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5579 (mm-30) REVERT: G 154 GLU cc_start: 0.7679 (pp20) cc_final: 0.6092 (pt0) REVERT: H 12 LEU cc_start: 0.7679 (tp) cc_final: 0.7416 (tt) REVERT: H 101 ASP cc_start: 0.6208 (m-30) cc_final: 0.5534 (m-30) REVERT: I 86 LYS cc_start: 0.6735 (tptt) cc_final: 0.6471 (tptt) REVERT: J 73 VAL cc_start: 0.9170 (p) cc_final: 0.8940 (m) REVERT: J 93 ILE cc_start: 0.8957 (pt) cc_final: 0.8599 (mm) REVERT: J 111 LYS cc_start: 0.7296 (mmtm) cc_final: 0.6521 (mmtm) REVERT: K 57 LEU cc_start: 0.8624 (mt) cc_final: 0.8383 (mt) REVERT: L 55 MET cc_start: 0.7060 (tpp) cc_final: 0.6442 (tpp) REVERT: N 20 MET cc_start: 0.7013 (tpp) cc_final: 0.6733 (tpp) REVERT: N 49 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7710 (mt-10) REVERT: N 102 PHE cc_start: 0.6164 (m-10) cc_final: 0.5938 (m-10) REVERT: O 45 SER cc_start: 0.8084 (m) cc_final: 0.7824 (p) REVERT: Q 88 GLU cc_start: 0.6335 (mm-30) cc_final: 0.5987 (mm-30) REVERT: Q 106 THR cc_start: 0.7979 (m) cc_final: 0.6956 (m) REVERT: S 38 TYR cc_start: 0.7590 (m-10) cc_final: 0.7322 (m-10) REVERT: S 77 ASP cc_start: 0.8358 (p0) cc_final: 0.7614 (p0) REVERT: T 1 MET cc_start: 0.4909 (ptm) cc_final: 0.4647 (ptm) REVERT: T 8 LEU cc_start: 0.7437 (mp) cc_final: 0.6941 (mt) REVERT: U 38 ILE cc_start: 0.6490 (mm) cc_final: 0.6240 (mm) REVERT: V 26 PHE cc_start: 0.7911 (p90) cc_final: 0.7449 (p90) REVERT: W 13 ARG cc_start: 0.6848 (tpt170) cc_final: 0.6242 (ttt-90) REVERT: W 67 LYS cc_start: 0.7120 (mtpp) cc_final: 0.6752 (mtpp) REVERT: W 77 LYS cc_start: 0.8171 (mttt) cc_final: 0.7827 (mttm) REVERT: Y 13 GLU cc_start: 0.4893 (tt0) cc_final: 0.4601 (tt0) REVERT: Z 20 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7202 (ttmt) REVERT: Z 46 MET cc_start: 0.8306 (mmm) cc_final: 0.7935 (tpp) REVERT: Z 55 LYS cc_start: 0.6992 (tttp) cc_final: 0.6783 (ttpp) outliers start: 2 outliers final: 0 residues processed: 750 average time/residue: 0.9306 time to fit residues: 1183.4662 Evaluate side-chains 539 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 568 optimal weight: 7.9990 chunk 387 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 508 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 582 optimal weight: 4.9990 chunk 471 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 612 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 18 HIS ** 5 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 227 GLN 6 294 ASN 6 355 GLN 6 368 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN D 49 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN I 30 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 105573 Z= 0.230 Angle : 0.687 12.167 157541 Z= 0.349 Chirality : 0.038 0.354 20115 Planarity : 0.005 0.069 8752 Dihedral : 25.086 179.310 51730 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 1.26 % Allowed : 11.97 % Favored : 86.77 % Rotamer: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.12), residues: 4126 helix: -1.33 (0.15), residues: 1039 sheet: -2.67 (0.18), residues: 629 loop : -2.44 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 247 HIS 0.010 0.002 HIS R 12 PHE 0.025 0.002 PHE J 4 TYR 0.024 0.002 TYR 6 205 ARG 0.024 0.001 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 725 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 HIS cc_start: 0.5143 (OUTLIER) cc_final: 0.4771 (t-170) REVERT: 1 25 ASN cc_start: 0.8470 (t0) cc_final: 0.8261 (t0) REVERT: 2 4 THR cc_start: 0.8496 (p) cc_final: 0.8194 (t) REVERT: 2 31 LEU cc_start: 0.8831 (pp) cc_final: 0.8067 (mp) REVERT: 4 28 SER cc_start: 0.7288 (m) cc_final: 0.7045 (t) REVERT: 5 1 MET cc_start: 0.3832 (mmp) cc_final: 0.3184 (mmt) REVERT: 5 121 MET cc_start: 0.3845 (mmt) cc_final: 0.3388 (mmp) REVERT: C 82 TYR cc_start: 0.5922 (t80) cc_final: 0.5339 (t80) REVERT: D 146 ILE cc_start: 0.8488 (pt) cc_final: 0.8247 (pt) REVERT: G 9 VAL cc_start: 0.7076 (t) cc_final: 0.6726 (t) REVERT: G 31 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5234 (mm-30) REVERT: G 154 GLU cc_start: 0.7589 (pp20) cc_final: 0.6090 (pt0) REVERT: H 12 LEU cc_start: 0.7675 (tp) cc_final: 0.7468 (tt) REVERT: I 86 LYS cc_start: 0.6735 (tptt) cc_final: 0.6475 (tptt) REVERT: J 30 THR cc_start: 0.7423 (p) cc_final: 0.7041 (p) REVERT: J 93 ILE cc_start: 0.8998 (pt) cc_final: 0.8643 (mm) REVERT: K 57 LEU cc_start: 0.8584 (mt) cc_final: 0.8370 (mt) REVERT: L 135 ILE cc_start: 0.8303 (pt) cc_final: 0.8057 (pt) REVERT: M 136 MET cc_start: 0.6464 (tmm) cc_final: 0.6205 (tmm) REVERT: N 49 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7803 (mt-10) REVERT: N 75 ILE cc_start: 0.8368 (mm) cc_final: 0.8116 (mm) REVERT: N 107 ASN cc_start: 0.8487 (t0) cc_final: 0.7073 (m110) REVERT: O 18 LEU cc_start: 0.7705 (mp) cc_final: 0.7398 (mm) REVERT: O 45 SER cc_start: 0.7937 (m) cc_final: 0.7699 (p) REVERT: S 77 ASP cc_start: 0.8382 (p0) cc_final: 0.7395 (p0) REVERT: T 1 MET cc_start: 0.4714 (ptm) cc_final: 0.4360 (ptm) REVERT: T 8 LEU cc_start: 0.7550 (mp) cc_final: 0.7058 (mt) REVERT: V 26 PHE cc_start: 0.8211 (p90) cc_final: 0.7926 (p90) REVERT: V 89 ILE cc_start: 0.6844 (pt) cc_final: 0.6606 (pt) REVERT: W 13 ARG cc_start: 0.6778 (tpt170) cc_final: 0.6263 (ttt-90) REVERT: W 36 ILE cc_start: 0.8417 (mm) cc_final: 0.8026 (mm) REVERT: W 77 LYS cc_start: 0.8177 (mttt) cc_final: 0.7816 (mttm) REVERT: W 79 ILE cc_start: 0.9189 (tp) cc_final: 0.8783 (tt) REVERT: Y 30 MET cc_start: 0.7111 (tpt) cc_final: 0.6798 (tpp) REVERT: Z 20 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7115 (ttmt) REVERT: Z 23 LEU cc_start: 0.8224 (pp) cc_final: 0.8022 (pp) REVERT: Z 46 MET cc_start: 0.8250 (mmm) cc_final: 0.7876 (tpp) outliers start: 2 outliers final: 0 residues processed: 727 average time/residue: 0.9250 time to fit residues: 1148.6731 Evaluate side-chains 539 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 229 optimal weight: 20.0000 chunk 614 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 400 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 683 optimal weight: 9.9990 chunk 567 optimal weight: 20.0000 chunk 316 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 225 optimal weight: 40.0000 chunk 358 optimal weight: 20.0000 overall best weight: 15.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 ASN 6 227 GLN ** 6 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN H 73 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.8536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.223 105573 Z= 0.491 Angle : 0.956 11.488 157541 Z= 0.477 Chirality : 0.049 0.361 20115 Planarity : 0.007 0.081 8752 Dihedral : 25.430 179.691 51730 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 41.08 Ramachandran Plot: Outliers : 1.24 % Allowed : 14.83 % Favored : 83.93 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.72 (0.11), residues: 4126 helix: -1.88 (0.14), residues: 1031 sheet: -2.87 (0.18), residues: 601 loop : -2.73 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP T 80 HIS 0.013 0.003 HIS 6 82 PHE 0.036 0.003 PHE J 4 TYR 0.036 0.003 TYR 6 205 ARG 0.011 0.001 ARG J 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 657 time to evaluate : 4.485 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: 2 11 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7496 (mmtp) REVERT: 2 31 LEU cc_start: 0.9052 (pp) cc_final: 0.8245 (mp) REVERT: 5 1 MET cc_start: 0.4443 (mmp) cc_final: 0.3483 (mmt) REVERT: 6 122 LEU cc_start: 0.8133 (tt) cc_final: 0.7565 (tp) REVERT: 6 169 ASN cc_start: 0.7471 (m-40) cc_final: 0.7214 (m-40) REVERT: D 165 MET cc_start: 0.7979 (tpp) cc_final: 0.7750 (tpp) REVERT: E 108 ILE cc_start: 0.8690 (pt) cc_final: 0.8358 (tp) REVERT: G 154 GLU cc_start: 0.8038 (pp20) cc_final: 0.6265 (pt0) REVERT: I 86 LYS cc_start: 0.7057 (tptt) cc_final: 0.6827 (tptt) REVERT: J 86 GLN cc_start: 0.9014 (pp30) cc_final: 0.8756 (pp30) REVERT: K 5 THR cc_start: 0.8999 (m) cc_final: 0.8468 (m) REVERT: L 55 MET cc_start: 0.6561 (mmm) cc_final: 0.6359 (mmt) REVERT: N 49 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7823 (mp0) REVERT: N 81 ASN cc_start: 0.8265 (m-40) cc_final: 0.7981 (m110) REVERT: N 107 ASN cc_start: 0.8768 (t0) cc_final: 0.7302 (m110) REVERT: P 55 HIS cc_start: 0.6528 (m90) cc_final: 0.6072 (m90) REVERT: S 77 ASP cc_start: 0.8439 (p0) cc_final: 0.7654 (p0) REVERT: S 92 ARG cc_start: 0.6459 (ttp-170) cc_final: 0.6218 (tmm-80) REVERT: T 1 MET cc_start: 0.5381 (ptm) cc_final: 0.5131 (ptm) REVERT: V 26 PHE cc_start: 0.8651 (p90) cc_final: 0.8266 (p90) REVERT: V 82 TYR cc_start: 0.7330 (p90) cc_final: 0.6857 (p90) REVERT: V 89 ILE cc_start: 0.6874 (pt) cc_final: 0.6483 (pt) REVERT: W 13 ARG cc_start: 0.7258 (tpt170) cc_final: 0.6591 (ttp80) REVERT: W 69 GLU cc_start: 0.7621 (pm20) cc_final: 0.7323 (pm20) REVERT: W 77 LYS cc_start: 0.7885 (mttt) cc_final: 0.7625 (mttt) REVERT: W 82 GLU cc_start: 0.5854 (mt-10) cc_final: 0.5537 (mt-10) REVERT: Y 30 MET cc_start: 0.7463 (tpt) cc_final: 0.7077 (tpp) REVERT: Z 20 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7299 (ttmt) outliers start: 0 outliers final: 0 residues processed: 657 average time/residue: 0.9213 time to fit residues: 1040.1282 Evaluate side-chains 490 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 658 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 389 optimal weight: 20.0000 chunk 498 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 575 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 680 optimal weight: 8.9990 chunk 425 optimal weight: 5.9990 chunk 414 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 33 HIS ** 6 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 ASN 6 294 ASN 6 355 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN H 145 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.8901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 105573 Z= 0.240 Angle : 0.713 11.986 157541 Z= 0.362 Chirality : 0.039 0.343 20115 Planarity : 0.005 0.074 8752 Dihedral : 25.180 179.985 51730 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.46 % Favored : 87.30 % Rotamer: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.35 (0.12), residues: 4126 helix: -1.42 (0.15), residues: 1033 sheet: -2.57 (0.19), residues: 593 loop : -2.60 (0.11), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP T 80 HIS 0.012 0.002 HIS 1 18 PHE 0.048 0.002 PHE W 68 TYR 0.030 0.002 TYR 6 205 ARG 0.018 0.001 ARG U 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 683 time to evaluate : 4.452 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: 1 50 GLU cc_start: 0.6784 (pp20) cc_final: 0.6412 (pp20) REVERT: 2 4 THR cc_start: 0.8644 (p) cc_final: 0.8371 (t) REVERT: 2 28 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7418 (tpp80) REVERT: 2 31 LEU cc_start: 0.8824 (pp) cc_final: 0.8106 (mp) REVERT: 5 1 MET cc_start: 0.3927 (mmp) cc_final: 0.2948 (mmt) REVERT: 6 71 LYS cc_start: 0.8240 (pptt) cc_final: 0.7954 (tmtt) REVERT: D 146 ILE cc_start: 0.8682 (pt) cc_final: 0.8475 (pt) REVERT: E 199 MET cc_start: 0.5166 (tpp) cc_final: 0.4959 (tpp) REVERT: G 31 GLU cc_start: 0.5616 (mm-30) cc_final: 0.4980 (mm-30) REVERT: G 76 ILE cc_start: 0.8447 (pt) cc_final: 0.8131 (tt) REVERT: G 80 GLU cc_start: 0.6246 (pm20) cc_final: 0.5878 (pm20) REVERT: G 127 GLN cc_start: 0.7338 (pm20) cc_final: 0.7064 (pm20) REVERT: G 154 GLU cc_start: 0.7736 (pp20) cc_final: 0.6498 (pt0) REVERT: H 15 LEU cc_start: 0.6708 (mt) cc_final: 0.6423 (mt) REVERT: I 86 LYS cc_start: 0.6794 (tptt) cc_final: 0.6519 (tptt) REVERT: J 30 THR cc_start: 0.7342 (p) cc_final: 0.6921 (p) REVERT: J 52 ASP cc_start: 0.7992 (m-30) cc_final: 0.7601 (m-30) REVERT: J 71 ASP cc_start: 0.6750 (t70) cc_final: 0.6470 (t70) REVERT: J 111 LYS cc_start: 0.7255 (mmtm) cc_final: 0.7010 (mmtt) REVERT: J 120 ARG cc_start: 0.7784 (ttt-90) cc_final: 0.6995 (mtt180) REVERT: K 6 MET cc_start: 0.7923 (mtt) cc_final: 0.7650 (mtm) REVERT: K 57 LEU cc_start: 0.8650 (mt) cc_final: 0.8238 (mt) REVERT: L 135 ILE cc_start: 0.8357 (pt) cc_final: 0.8110 (pt) REVERT: N 49 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7787 (mp0) REVERT: Q 59 LEU cc_start: 0.8161 (pp) cc_final: 0.7740 (tt) REVERT: Q 106 THR cc_start: 0.8370 (m) cc_final: 0.8056 (m) REVERT: S 77 ASP cc_start: 0.8148 (p0) cc_final: 0.7825 (p0) REVERT: S 92 ARG cc_start: 0.6327 (ttp-170) cc_final: 0.6043 (tmm-80) REVERT: T 1 MET cc_start: 0.4998 (ptm) cc_final: 0.4700 (ptm) REVERT: V 26 PHE cc_start: 0.8717 (p90) cc_final: 0.8250 (p90) REVERT: V 86 LEU cc_start: 0.7851 (mp) cc_final: 0.7370 (mp) REVERT: V 89 ILE cc_start: 0.6751 (pt) cc_final: 0.6433 (pt) REVERT: W 13 ARG cc_start: 0.6915 (tpt170) cc_final: 0.6405 (ttt-90) REVERT: W 77 LYS cc_start: 0.8021 (mttt) cc_final: 0.7802 (mttt) REVERT: W 82 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5663 (mt-10) REVERT: Y 30 MET cc_start: 0.7609 (tpt) cc_final: 0.7240 (tpp) REVERT: Z 20 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7351 (ttmt) REVERT: Z 23 LEU cc_start: 0.8244 (pp) cc_final: 0.7939 (mt) outliers start: 1 outliers final: 0 residues processed: 684 average time/residue: 0.9186 time to fit residues: 1083.5753 Evaluate side-chains 515 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 420 optimal weight: 30.0000 chunk 271 optimal weight: 20.0000 chunk 406 optimal weight: 8.9990 chunk 204 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 432 optimal weight: 8.9990 chunk 463 optimal weight: 7.9990 chunk 336 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 534 optimal weight: 2.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 294 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 105573 Z= 0.263 Angle : 0.713 10.002 157541 Z= 0.362 Chirality : 0.039 0.345 20115 Planarity : 0.005 0.077 8752 Dihedral : 25.073 179.599 51730 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 28.75 Ramachandran Plot: Outliers : 1.24 % Allowed : 12.87 % Favored : 85.89 % Rotamer: Outliers : 0.03 % Allowed : 1.30 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.12), residues: 4126 helix: -1.25 (0.15), residues: 1023 sheet: -2.57 (0.18), residues: 583 loop : -2.62 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP T 80 HIS 0.011 0.002 HIS 1 45 PHE 0.026 0.002 PHE J 4 TYR 0.036 0.002 TYR 6 205 ARG 0.036 0.001 ARG 5 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 645 time to evaluate : 4.780 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: 2 4 THR cc_start: 0.8704 (p) cc_final: 0.8412 (t) REVERT: 2 11 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7796 (tptm) REVERT: 2 31 LEU cc_start: 0.8920 (pp) cc_final: 0.8195 (mp) REVERT: 5 1 MET cc_start: 0.4206 (mmp) cc_final: 0.2888 (mmt) REVERT: 6 56 TYR cc_start: 0.7069 (m-80) cc_final: 0.6832 (m-80) REVERT: 6 71 LYS cc_start: 0.8138 (pptt) cc_final: 0.7889 (tmtt) REVERT: 6 169 ASN cc_start: 0.7570 (m110) cc_final: 0.7330 (m-40) REVERT: D 146 ILE cc_start: 0.8565 (pt) cc_final: 0.8332 (pt) REVERT: G 76 ILE cc_start: 0.8480 (pt) cc_final: 0.8011 (tt) REVERT: G 127 GLN cc_start: 0.7413 (pm20) cc_final: 0.7165 (pm20) REVERT: G 154 GLU cc_start: 0.8011 (pp20) cc_final: 0.6243 (pt0) REVERT: H 15 LEU cc_start: 0.7115 (mt) cc_final: 0.6597 (mp) REVERT: I 86 LYS cc_start: 0.6828 (tptt) cc_final: 0.6569 (tptt) REVERT: J 30 THR cc_start: 0.7658 (p) cc_final: 0.7345 (p) REVERT: J 120 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7028 (mtt180) REVERT: K 5 THR cc_start: 0.8380 (m) cc_final: 0.8135 (m) REVERT: K 6 MET cc_start: 0.8136 (mtt) cc_final: 0.7777 (mtm) REVERT: K 21 ILE cc_start: 0.7613 (pt) cc_final: 0.6285 (pt) REVERT: K 57 LEU cc_start: 0.8730 (mt) cc_final: 0.8460 (mt) REVERT: L 55 MET cc_start: 0.6616 (mmm) cc_final: 0.6350 (mmt) REVERT: N 49 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7836 (mp0) REVERT: N 110 MET cc_start: 0.8684 (mmm) cc_final: 0.7977 (mmm) REVERT: S 77 ASP cc_start: 0.8059 (p0) cc_final: 0.7795 (p0) REVERT: S 92 ARG cc_start: 0.6392 (ttp-170) cc_final: 0.6156 (tmm-80) REVERT: T 1 MET cc_start: 0.5203 (ptm) cc_final: 0.4762 (ptm) REVERT: V 26 PHE cc_start: 0.8702 (p90) cc_final: 0.8215 (p90) REVERT: V 89 ILE cc_start: 0.6652 (pt) cc_final: 0.6433 (pt) REVERT: W 13 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6428 (ttt-90) REVERT: W 77 LYS cc_start: 0.7991 (mttt) cc_final: 0.7407 (mttm) REVERT: Y 30 MET cc_start: 0.7728 (tpt) cc_final: 0.7285 (tpp) REVERT: Z 20 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7301 (ttmt) REVERT: Z 23 LEU cc_start: 0.8388 (pp) cc_final: 0.8034 (mt) outliers start: 1 outliers final: 1 residues processed: 646 average time/residue: 0.9024 time to fit residues: 1011.4859 Evaluate side-chains 498 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 497 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 618 optimal weight: 3.9990 chunk 651 optimal weight: 20.0000 chunk 594 optimal weight: 20.0000 chunk 634 optimal weight: 2.9990 chunk 381 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 497 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 573 optimal weight: 1.9990 chunk 599 optimal weight: 7.9990 chunk 631 optimal weight: 10.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN 1 25 ASN ** 6 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 294 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN G 138 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.9520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 105573 Z= 0.203 Angle : 0.653 12.067 157541 Z= 0.332 Chirality : 0.036 0.419 20115 Planarity : 0.005 0.074 8752 Dihedral : 24.928 179.342 51730 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 1.24 % Allowed : 10.64 % Favored : 88.12 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.12), residues: 4126 helix: -1.10 (0.16), residues: 1022 sheet: -2.34 (0.19), residues: 574 loop : -2.51 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 80 HIS 0.008 0.001 HIS J 77 PHE 0.026 0.002 PHE J 4 TYR 0.032 0.002 TYR 6 205 ARG 0.016 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 657 time to evaluate : 4.508 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: 2 4 THR cc_start: 0.8633 (p) cc_final: 0.8244 (t) REVERT: 2 11 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7959 (tptm) REVERT: 2 28 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7845 (mtp180) REVERT: 2 31 LEU cc_start: 0.8901 (pp) cc_final: 0.8280 (mp) REVERT: 5 1 MET cc_start: 0.4015 (mmp) cc_final: 0.3185 (mmt) REVERT: 6 56 TYR cc_start: 0.7016 (m-80) cc_final: 0.6744 (m-80) REVERT: D 20 VAL cc_start: 0.8487 (t) cc_final: 0.7816 (t) REVERT: D 146 ILE cc_start: 0.8522 (pt) cc_final: 0.8273 (pt) REVERT: F 25 MET cc_start: 0.5842 (mmm) cc_final: 0.5033 (mmm) REVERT: G 31 GLU cc_start: 0.5665 (mm-30) cc_final: 0.4660 (mm-30) REVERT: G 76 ILE cc_start: 0.8426 (pt) cc_final: 0.8060 (tt) REVERT: G 80 GLU cc_start: 0.5848 (pm20) cc_final: 0.5340 (pm20) REVERT: G 154 GLU cc_start: 0.7792 (pp20) cc_final: 0.6163 (pt0) REVERT: H 15 LEU cc_start: 0.6890 (mt) cc_final: 0.6633 (mt) REVERT: I 86 LYS cc_start: 0.6690 (tptt) cc_final: 0.6485 (tptt) REVERT: J 30 THR cc_start: 0.7645 (p) cc_final: 0.7302 (p) REVERT: J 118 MET cc_start: 0.8690 (mpp) cc_final: 0.8378 (mpp) REVERT: J 120 ARG cc_start: 0.7456 (ttt-90) cc_final: 0.6954 (mtt180) REVERT: K 6 MET cc_start: 0.7987 (mtt) cc_final: 0.7546 (mtm) REVERT: K 21 ILE cc_start: 0.7231 (pt) cc_final: 0.6830 (pt) REVERT: K 57 LEU cc_start: 0.8744 (mt) cc_final: 0.8512 (mt) REVERT: L 135 ILE cc_start: 0.8287 (pt) cc_final: 0.8063 (pt) REVERT: M 128 THR cc_start: 0.7310 (t) cc_final: 0.7041 (t) REVERT: N 49 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7730 (mp0) REVERT: N 110 MET cc_start: 0.8611 (mmm) cc_final: 0.7933 (mmm) REVERT: Q 17 LEU cc_start: 0.8555 (mm) cc_final: 0.8305 (mt) REVERT: Q 59 LEU cc_start: 0.8103 (pp) cc_final: 0.7633 (tt) REVERT: R 74 ILE cc_start: 0.9064 (mt) cc_final: 0.8826 (mt) REVERT: S 77 ASP cc_start: 0.7682 (p0) cc_final: 0.7408 (p0) REVERT: T 1 MET cc_start: 0.5191 (ptm) cc_final: 0.4759 (ptm) REVERT: T 24 MET cc_start: 0.6884 (mmm) cc_final: 0.6539 (mtt) REVERT: V 26 PHE cc_start: 0.8637 (p90) cc_final: 0.8343 (p90) REVERT: W 13 ARG cc_start: 0.6829 (tpt170) cc_final: 0.6286 (ttt-90) REVERT: W 77 LYS cc_start: 0.7923 (mttt) cc_final: 0.7471 (mttm) REVERT: Y 1 MET cc_start: 0.2421 (ppp) cc_final: 0.2206 (ppp) REVERT: Y 30 MET cc_start: 0.7738 (tpt) cc_final: 0.7315 (tpp) REVERT: Z 20 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7287 (ttmt) REVERT: Z 23 LEU cc_start: 0.8380 (pp) cc_final: 0.8037 (mt) outliers start: 2 outliers final: 0 residues processed: 659 average time/residue: 0.9027 time to fit residues: 1025.5115 Evaluate side-chains 530 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 4.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 416 optimal weight: 40.0000 chunk 670 optimal weight: 30.0000 chunk 409 optimal weight: 0.6980 chunk 318 optimal weight: 20.0000 chunk 466 optimal weight: 8.9990 chunk 703 optimal weight: 0.5980 chunk 647 optimal weight: 4.9990 chunk 560 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 432 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 30 GLN E 92 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN P 11 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.9808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 105573 Z= 0.148 Angle : 0.600 11.145 157541 Z= 0.304 Chirality : 0.033 0.340 20115 Planarity : 0.005 0.060 8752 Dihedral : 24.690 179.696 51730 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.60 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.12), residues: 4126 helix: -0.87 (0.16), residues: 1007 sheet: -1.95 (0.20), residues: 570 loop : -2.40 (0.11), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 96 HIS 0.022 0.001 HIS F 4 PHE 0.048 0.002 PHE 6 267 TYR 0.025 0.001 TYR H 25 ARG 0.008 0.001 ARG W 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 4.443 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: 1 6 GLU cc_start: 0.6673 (pp20) cc_final: 0.6379 (pp20) REVERT: 1 24 LYS cc_start: 0.7248 (mmmt) cc_final: 0.7006 (mmmt) REVERT: 2 4 THR cc_start: 0.8420 (p) cc_final: 0.8051 (t) REVERT: 2 11 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7897 (tptt) REVERT: 2 31 LEU cc_start: 0.8821 (pp) cc_final: 0.8599 (tp) REVERT: 5 1 MET cc_start: 0.3466 (mmp) cc_final: 0.2612 (mmt) REVERT: 6 71 LYS cc_start: 0.8236 (pptt) cc_final: 0.7883 (tmmt) REVERT: D 18 ASP cc_start: 0.7466 (p0) cc_final: 0.7215 (p0) REVERT: D 101 PHE cc_start: 0.7720 (m-80) cc_final: 0.7380 (m-80) REVERT: D 146 ILE cc_start: 0.8461 (pt) cc_final: 0.8106 (pt) REVERT: G 31 GLU cc_start: 0.5683 (mm-30) cc_final: 0.4541 (mm-30) REVERT: G 76 ILE cc_start: 0.8278 (pt) cc_final: 0.7773 (tt) REVERT: G 80 GLU cc_start: 0.5735 (pm20) cc_final: 0.5202 (pm20) REVERT: G 154 GLU cc_start: 0.7471 (pp20) cc_final: 0.6095 (pt0) REVERT: I 86 LYS cc_start: 0.6674 (tptt) cc_final: 0.6397 (tptt) REVERT: J 30 THR cc_start: 0.8101 (p) cc_final: 0.7829 (p) REVERT: J 118 MET cc_start: 0.8652 (mpp) cc_final: 0.8391 (mpp) REVERT: J 120 ARG cc_start: 0.6907 (ttt-90) cc_final: 0.6445 (mtt90) REVERT: K 57 LEU cc_start: 0.8596 (mt) cc_final: 0.8287 (mt) REVERT: L 55 MET cc_start: 0.6551 (mmm) cc_final: 0.6295 (mmt) REVERT: L 135 ILE cc_start: 0.8249 (pt) cc_final: 0.8049 (pt) REVERT: N 49 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7785 (mp0) REVERT: N 110 MET cc_start: 0.8645 (mmm) cc_final: 0.7950 (mmm) REVERT: Q 59 LEU cc_start: 0.7935 (pp) cc_final: 0.7540 (tt) REVERT: Q 87 VAL cc_start: 0.7247 (t) cc_final: 0.6985 (t) REVERT: Q 88 GLU cc_start: 0.7237 (pm20) cc_final: 0.6682 (mm-30) REVERT: R 74 ILE cc_start: 0.9001 (mt) cc_final: 0.8777 (mt) REVERT: S 77 ASP cc_start: 0.7341 (p0) cc_final: 0.7046 (p0) REVERT: S 102 HIS cc_start: 0.7672 (m-70) cc_final: 0.7106 (m-70) REVERT: S 104 THR cc_start: 0.7734 (m) cc_final: 0.7405 (p) REVERT: T 1 MET cc_start: 0.5011 (ptm) cc_final: 0.4103 (ptm) REVERT: T 24 MET cc_start: 0.6601 (mmm) cc_final: 0.6245 (mtt) REVERT: T 77 ARG cc_start: 0.8110 (tpm170) cc_final: 0.7661 (tpm170) REVERT: U 17 ASP cc_start: 0.4576 (t70) cc_final: 0.3614 (t0) REVERT: U 38 ILE cc_start: 0.6654 (tt) cc_final: 0.6178 (tt) REVERT: V 57 TYR cc_start: 0.6902 (m-80) cc_final: 0.6494 (m-80) REVERT: W 13 ARG cc_start: 0.6853 (tpt170) cc_final: 0.6230 (ttt-90) REVERT: W 69 GLU cc_start: 0.7031 (pm20) cc_final: 0.6820 (pm20) REVERT: W 77 LYS cc_start: 0.7686 (mttt) cc_final: 0.7128 (mttm) REVERT: X 42 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6246 (mm-30) REVERT: Y 27 ASN cc_start: 0.6404 (t0) cc_final: 0.6191 (t0) REVERT: Y 30 MET cc_start: 0.7543 (tpt) cc_final: 0.7109 (tpp) REVERT: Y 42 LEU cc_start: 0.8165 (mt) cc_final: 0.7821 (tp) REVERT: Z 20 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7326 (ttmt) REVERT: Z 23 LEU cc_start: 0.8370 (pp) cc_final: 0.8107 (mp) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.9252 time to fit residues: 1095.7253 Evaluate side-chains 541 residues out of total 3393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 444 optimal weight: 9.9990 chunk 596 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 516 optimal weight: 0.0970 chunk 82 optimal weight: 50.0000 chunk 155 optimal weight: 30.0000 chunk 560 optimal weight: 0.0170 chunk 234 optimal weight: 20.0000 chunk 576 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 overall best weight: 4.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 9 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 80 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS T 91 GLN V 24 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045406 restraints weight = 577904.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046767 restraints weight = 223571.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047549 restraints weight = 119005.552| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.9925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 105573 Z= 0.173 Angle : 0.601 13.039 157541 Z= 0.304 Chirality : 0.033 0.343 20115 Planarity : 0.005 0.061 8752 Dihedral : 24.630 179.929 51730 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.16 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.12), residues: 4126 helix: -0.79 (0.16), residues: 1036 sheet: -1.95 (0.20), residues: 596 loop : -2.39 (0.11), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP Q 60 HIS 0.012 0.001 HIS Q 13 PHE 0.032 0.002 PHE Q 56 TYR 0.020 0.002 TYR Q 31 ARG 0.009 0.001 ARG 5 7 =============================================================================== Job complete usr+sys time: 18615.03 seconds wall clock time: 333 minutes 27.26 seconds (20007.26 seconds total)