Starting phenix.real_space_refine on Sun Sep 29 19:29:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/09_2024/6he7_0211.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/09_2024/6he7_0211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/09_2024/6he7_0211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/09_2024/6he7_0211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/09_2024/6he7_0211.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he7_0211/09_2024/6he7_0211.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 15113 2.51 5 N 3990 2.21 5 O 4634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 369 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23821 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "C" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "D" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "E" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "F" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "G" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1850 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "1" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1553 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Time building chain proxies: 14.05, per 1000 atoms: 0.59 Number of scatterers: 23821 At special positions: 0 Unit cell: (134, 134, 104.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 4634 8.00 N 3990 7.00 C 15113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 2.9 seconds 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 30 sheets defined 43.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.745A pdb=" N PHE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 4.041A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 Processing helix chain 'A' and resid 225 through 244 Proline residue: A 231 - end of helix removed outlier: 3.775A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.535A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.585A pdb=" N ILE B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 225 through 245 removed outlier: 3.963A pdb=" N LYS B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.514A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 81 through 104 removed outlier: 3.678A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.568A pdb=" N TYR C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.976A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 225 through 244 Proline residue: C 231 - end of helix removed outlier: 3.537A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.627A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 244 removed outlier: 4.004A pdb=" N LYS D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) Proline residue: D 231 - end of helix removed outlier: 3.659A pdb=" N ARG D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.691A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.761A pdb=" N ALA E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.563A pdb=" N SER E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 244 Proline residue: E 231 - end of helix removed outlier: 3.668A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 81 through 104 removed outlier: 3.727A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.544A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.688A pdb=" N LYS F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 225 through 243 Proline residue: F 231 - end of helix removed outlier: 3.802A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.623A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.659A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 201 removed outlier: 3.545A pdb=" N ILE G 200 " --> pdb=" O MET G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 244 Proline residue: G 231 - end of helix removed outlier: 3.621A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) Processing helix chain '1' and resid 60 through 82 Processing helix chain '1' and resid 86 through 101 Processing helix chain '1' and resid 143 through 155 removed outlier: 4.175A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL 1 150 " --> pdb=" O THR 1 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP 1 153 " --> pdb=" O GLY 1 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG 1 154 " --> pdb=" O VAL 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 177 removed outlier: 4.247A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 1 167 " --> pdb=" O GLU 1 163 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA 1 175 " --> pdb=" O ALA 1 171 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET 1 176 " --> pdb=" O ILE 1 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS 1 177 " --> pdb=" O TYR 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 206 removed outlier: 4.485A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 1 204 " --> pdb=" O SER 1 200 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.775A pdb=" N ALA 2 63 " --> pdb=" O SER 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 Processing helix chain '2' and resid 143 through 155 removed outlier: 4.215A pdb=" N GLY 2 149 " --> pdb=" O LEU 2 145 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG 2 154 " --> pdb=" O VAL 2 150 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 179 removed outlier: 4.194A pdb=" N ARG 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP 2 179 " --> pdb=" O ALA 2 175 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 208 removed outlier: 4.511A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE 2 207 " --> pdb=" O GLU 2 203 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 Processing helix chain '3' and resid 86 through 101 removed outlier: 3.564A pdb=" N ASN 3 99 " --> pdb=" O SER 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 143 through 155 removed outlier: 3.798A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG 3 154 " --> pdb=" O VAL 3 150 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 177 Processing helix chain '3' and resid 200 through 212 removed outlier: 3.501A pdb=" N GLN 3 206 " --> pdb=" O GLU 3 202 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE 3 207 " --> pdb=" O GLU 3 203 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS 3 210 " --> pdb=" O GLN 3 206 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE 3 211 " --> pdb=" O ILE 3 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG 3 212 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) Processing helix chain '4' and resid 59 through 82 removed outlier: 4.239A pdb=" N ALA 4 63 " --> pdb=" O SER 4 59 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN 4 64 " --> pdb=" O VAL 4 60 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE 4 65 " --> pdb=" O GLY 4 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU 4 66 " --> pdb=" O ASP 4 62 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 4 68 " --> pdb=" O GLN 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 removed outlier: 3.566A pdb=" N ILE 4 90 " --> pdb=" O THR 4 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) Processing helix chain '4' and resid 143 through 152 Processing helix chain '4' and resid 160 through 179 removed outlier: 3.549A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 4 179 " --> pdb=" O ALA 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 205 removed outlier: 3.826A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) Processing helix chain '4' and resid 206 through 208 No H-bonds generated for 'chain '4' and resid 206 through 208' Processing helix chain '5' and resid 59 through 82 Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 155 removed outlier: 3.981A pdb=" N ARG 5 154 " --> pdb=" O VAL 5 150 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.776A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) Processing helix chain '5' and resid 200 through 206 removed outlier: 3.830A pdb=" N GLN 5 206 " --> pdb=" O GLU 5 202 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.537A pdb=" N ALA 6 63 " --> pdb=" O SER 6 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG 6 68 " --> pdb=" O GLN 6 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.532A pdb=" N ALA 6 91 " --> pdb=" O VAL 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 104 No H-bonds generated for 'chain '6' and resid 102 through 104' Processing helix chain '6' and resid 143 through 155 removed outlier: 4.120A pdb=" N ASP 6 153 " --> pdb=" O GLY 6 149 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.537A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.090A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 82 removed outlier: 3.588A pdb=" N ALA 7 63 " --> pdb=" O SER 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 155 removed outlier: 3.595A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 160 through 176 removed outlier: 3.514A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 208 removed outlier: 4.415A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 7 207 " --> pdb=" O GLU 7 203 " (cutoff:3.500A) Processing helix chain '7' and resid 209 through 211 No H-bonds generated for 'chain '7' and resid 209 through 211' Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 3.885A pdb=" N GLY A 45 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.878A pdb=" N ILE A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.720A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.674A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.767A pdb=" N GLY C 45 " --> pdb=" O CYS C 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.984A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.567A pdb=" N GLY D 45 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 220 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 7.343A pdb=" N ILE D 67 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS D 69 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA D 76 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP D 151 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 4.205A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 220 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.465A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.599A pdb=" N ALA F 37 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 222 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.995A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 161 through 162 removed outlier: 4.175A pdb=" N VAL G 211 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.539A pdb=" N ILE G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU G 147 " --> pdb=" O TYR G 159 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 157 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 137 through 141 removed outlier: 3.669A pdb=" N GLY 1 22 " --> pdb=" O CYS 1 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1' and resid 45 through 49 removed outlier: 6.525A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY 1 113 " --> pdb=" O ALA 1 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 1 110 " --> pdb=" O ILE 1 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 14 through 18 Processing sheet with id=AB9, first strand: chain '2' and resid 31 through 32 removed outlier: 3.945A pdb=" N ALA 2 31 " --> pdb=" O SER 2 39 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER 2 39 " --> pdb=" O ALA 2 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '2' and resid 45 through 49 removed outlier: 6.948A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 14 through 18 Processing sheet with id=AC3, first strand: chain '3' and resid 45 through 49 removed outlier: 6.531A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER 3 121 " --> pdb=" O GLY 3 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 3 122 " --> pdb=" O GLU 3 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 137 through 138 removed outlier: 3.525A pdb=" N ALA 4 26 " --> pdb=" O VAL 4 15 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 45 through 49 removed outlier: 6.625A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER 4 121 " --> pdb=" O GLY 4 114 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE 4 122 " --> pdb=" O GLU 4 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 137 through 141 removed outlier: 6.543A pdb=" N THR 5 13 " --> pdb=" O GLU 5 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU 5 28 " --> pdb=" O THR 5 13 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET 5 25 " --> pdb=" O VAL 5 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 45 through 49 removed outlier: 6.794A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 137 through 138 Processing sheet with id=AC9, first strand: chain '6' and resid 45 through 49 removed outlier: 6.454A pdb=" N MET 6 52 " --> pdb=" O ILE 6 48 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '7' and resid 137 through 138 Processing sheet with id=AD2, first strand: chain '7' and resid 32 through 33 removed outlier: 3.507A pdb=" N PHE 7 36 " --> pdb=" O MET 7 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 45 through 49 removed outlier: 6.836A pdb=" N MET 7 52 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.01 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 17623 1.52 - 1.88: 6505 1.88 - 2.24: 13 2.24 - 2.61: 1 2.61 - 2.97: 1 Bond restraints: 24143 Sorted by residual: bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.968 -1.584 2.10e-02 2.27e+03 5.69e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.182 -0.798 2.10e-02 2.27e+03 1.44e+03 bond pdb=" CE1 PHE 5 211 " pdb=" CZ PHE 5 211 " ideal model delta sigma weight residual 1.382 2.264 -0.882 3.00e-02 1.11e+03 8.64e+02 bond pdb=" CD2 PHE 5 211 " pdb=" CE2 PHE 5 211 " ideal model delta sigma weight residual 1.382 2.225 -0.843 3.00e-02 1.11e+03 7.89e+02 bond pdb=" CE2 PHE 5 211 " pdb=" CZ PHE 5 211 " ideal model delta sigma weight residual 1.382 2.200 -0.818 3.00e-02 1.11e+03 7.44e+02 ... (remaining 24138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.77: 31969 8.77 - 17.53: 595 17.53 - 26.30: 4 26.30 - 35.06: 1 35.06 - 43.83: 2 Bond angle restraints: 32571 Sorted by residual: angle pdb=" O ASP C 181 " pdb=" C ASP C 181 " pdb=" N ASP C 182 " ideal model delta sigma weight residual 122.59 166.42 -43.83 1.33e+00 5.65e-01 1.09e+03 angle pdb=" CA ASP C 181 " pdb=" C ASP C 181 " pdb=" O ASP C 181 " ideal model delta sigma weight residual 120.51 84.84 35.67 1.43e+00 4.89e-01 6.22e+02 angle pdb=" CA ASP C 181 " pdb=" C ASP C 181 " pdb=" N ASP C 182 " ideal model delta sigma weight residual 116.84 84.96 31.88 1.71e+00 3.42e-01 3.48e+02 angle pdb=" N ASP C 182 " pdb=" CA ASP C 182 " pdb=" CB ASP C 182 " ideal model delta sigma weight residual 110.56 133.77 -23.21 1.86e+00 2.89e-01 1.56e+02 angle pdb=" N LYS A 66 " pdb=" CA LYS A 66 " pdb=" C LYS A 66 " ideal model delta sigma weight residual 114.62 100.61 14.01 1.14e+00 7.69e-01 1.51e+02 ... (remaining 32566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.74: 13908 24.74 - 49.48: 657 49.48 - 74.21: 203 74.21 - 98.95: 78 98.95 - 123.69: 1 Dihedral angle restraints: 14847 sinusoidal: 5992 harmonic: 8855 Sorted by residual: dihedral pdb=" CA VAL G 54 " pdb=" C VAL G 54 " pdb=" N GLY G 55 " pdb=" CA GLY G 55 " ideal model delta harmonic sigma weight residual 180.00 56.31 123.69 0 5.00e+00 4.00e-02 6.12e+02 dihedral pdb=" CA ARG G 53 " pdb=" C ARG G 53 " pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta harmonic sigma weight residual 180.00 112.64 67.36 0 5.00e+00 4.00e-02 1.81e+02 dihedral pdb=" CA LYS G 52 " pdb=" C LYS G 52 " pdb=" N ARG G 53 " pdb=" CA ARG G 53 " ideal model delta harmonic sigma weight residual 180.00 -117.93 -62.07 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 14844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2343 0.180 - 0.360: 1110 0.360 - 0.539: 289 0.539 - 0.719: 27 0.719 - 0.899: 4 Chirality restraints: 3773 Sorted by residual: chirality pdb=" CA THR 6 140 " pdb=" N THR 6 140 " pdb=" C THR 6 140 " pdb=" CB THR 6 140 " both_signs ideal model delta sigma weight residual False 2.53 1.63 0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" CA LEU 2 208 " pdb=" N LEU 2 208 " pdb=" C LEU 2 208 " pdb=" CB LEU 2 208 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA ARG D 219 " pdb=" N ARG D 219 " pdb=" C ARG D 219 " pdb=" CB ARG D 219 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 3770 not shown) Planarity restraints: 4193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 103 " -0.240 2.00e-02 2.50e+03 1.63e-01 5.32e+02 pdb=" CG TYR 4 103 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 103 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 103 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 103 " 0.195 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 103 " 0.147 2.00e-02 2.50e+03 pdb=" CZ TYR 4 103 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR 4 103 " -0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 197 " 0.315 2.00e-02 2.50e+03 1.62e-01 5.25e+02 pdb=" CG TYR 1 197 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 197 " -0.190 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 197 " -0.129 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 197 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 197 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR 1 197 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR 1 197 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 211 " 0.115 2.00e-02 2.50e+03 1.71e-01 5.10e+02 pdb=" CG PHE 5 211 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 211 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 211 " -0.228 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 211 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 211 " 0.320 2.00e-02 2.50e+03 pdb=" CZ PHE 5 211 " -0.114 2.00e-02 2.50e+03 ... (remaining 4190 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 961 2.64 - 3.21: 19098 3.21 - 3.77: 36443 3.77 - 4.34: 52672 4.34 - 4.90: 85789 Nonbonded interactions: 194963 Sorted by model distance: nonbonded pdb=" NH1 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.081 3.420 nonbonded pdb=" NE ARG 5 170 " pdb=" CD1 PHE 5 211 " model vdw 2.159 3.420 nonbonded pdb=" OE1 GLU 5 166 " pdb=" CE2 PHE 5 211 " model vdw 2.184 3.340 nonbonded pdb=" CZ ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.192 3.570 nonbonded pdb=" NH1 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.206 3.340 ... (remaining 194958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.330 Process input model: 51.690 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.130 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 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 : 0.039 1.584 24143 Z= 2.505 Angle : 3.601 43.828 32571 Z= 2.410 Chirality : 0.206 0.899 3773 Planarity : 0.030 0.298 4193 Dihedral : 17.647 123.688 9177 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 1.55 % Allowed : 5.58 % Favored : 92.87 % Rotamer: Outliers : 4.93 % Allowed : 10.89 % Favored : 84.18 % Cbeta Deviations : 7.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.44 (0.13), residues: 3031 helix: -0.35 (0.13), residues: 1211 sheet: -1.06 (0.18), residues: 620 loop : -3.29 (0.12), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.035 0.011 HIS C 73 PHE 0.320 0.039 PHE 5 211 TYR 0.315 0.050 TYR 1 197 ARG 0.084 0.012 ARG 3 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 669 time to evaluate : 2.498 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: B 141 VAL cc_start: 0.9124 (t) cc_final: 0.8870 (m) REVERT: C 104 ASP cc_start: 0.8250 (t70) cc_final: 0.7989 (t0) REVERT: C 141 VAL cc_start: 0.9226 (t) cc_final: 0.8984 (m) REVERT: D 111 GLU cc_start: 0.7408 (tp30) cc_final: 0.6757 (tp30) REVERT: D 129 VAL cc_start: 0.8767 (p) cc_final: 0.8474 (m) REVERT: D 203 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6856 (mt-10) REVERT: G 71 ASP cc_start: 0.7580 (t0) cc_final: 0.6916 (t0) REVERT: G 159 TYR cc_start: 0.8344 (m-80) cc_final: 0.8034 (m-80) REVERT: G 196 MET cc_start: 0.7652 (ttm) cc_final: 0.7358 (ttm) REVERT: 1 128 ILE cc_start: 0.3763 (OUTLIER) cc_final: 0.3506 (tt) REVERT: 2 72 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.7783 (mp) REVERT: 3 39 SER cc_start: 0.3347 (OUTLIER) cc_final: 0.2804 (t) REVERT: 3 40 LYS cc_start: 0.3887 (OUTLIER) cc_final: 0.2321 (tppt) REVERT: 3 137 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5916 (mm) REVERT: 4 71 LYS cc_start: 0.8276 (tttt) cc_final: 0.8000 (tttm) REVERT: 4 88 ARG cc_start: 0.7170 (ttp-110) cc_final: 0.6890 (ttm-80) REVERT: 4 134 GLU cc_start: 0.7099 (mp0) cc_final: 0.6898 (mp0) REVERT: 5 33 MET cc_start: -0.0386 (mtp) cc_final: -0.2142 (ppp) REVERT: 6 123 TYR cc_start: 0.8062 (m-80) cc_final: 0.7561 (m-80) REVERT: 7 84 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8688 (mmmm) REVERT: 7 205 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.4948 (mp0) outliers start: 125 outliers final: 29 residues processed: 762 average time/residue: 0.4353 time to fit residues: 480.9642 Evaluate side-chains 560 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 525 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain 1 residue 72 ILE Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 3 residue 39 SER Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 125 ILE Chi-restraints excluded: chain 3 residue 137 ILE Chi-restraints excluded: chain 4 residue 72 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 150 VAL Chi-restraints excluded: chain 5 residue 205 GLU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 105 PRO Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 103 TYR Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 175 optimal weight: 0.2980 chunk 273 optimal weight: 0.0050 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 169 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN D 23 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN E 23 GLN E 237 ASN G 73 HIS G 237 ASN 1 96 ASN 3 96 ASN 6 47 GLN 6 64 GLN 6 96 ASN 7 75 ASN 7 96 ASN 7 198 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.852 24143 Z= 0.960 Angle : 0.803 30.148 32571 Z= 0.440 Chirality : 0.049 0.269 3773 Planarity : 0.006 0.092 4193 Dihedral : 7.708 84.133 3457 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 3.24 % Allowed : 15.79 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3031 helix: 0.88 (0.14), residues: 1253 sheet: -0.57 (0.18), residues: 652 loop : -2.40 (0.15), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.032 0.002 PHE 5 211 TYR 0.020 0.002 TYR E 213 ARG 0.034 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 544 time to evaluate : 2.771 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: A 66 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7596 (mmtp) REVERT: B 205 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7948 (m) REVERT: B 239 ARG cc_start: 0.7555 (tpt170) cc_final: 0.7072 (tpt170) REVERT: C 95 GLU cc_start: 0.8360 (tp30) cc_final: 0.7928 (tp30) REVERT: C 104 ASP cc_start: 0.8154 (t70) cc_final: 0.7903 (t70) REVERT: C 105 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 56 SER cc_start: 0.7910 (p) cc_final: 0.7327 (p) REVERT: 1 84 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8133 (mtpp) REVERT: 2 17 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7614 (pt) REVERT: 2 155 PHE cc_start: 0.7200 (t80) cc_final: 0.6895 (t80) REVERT: 3 106 TYR cc_start: 0.3221 (OUTLIER) cc_final: 0.1966 (t80) REVERT: 4 33 MET cc_start: -0.1165 (OUTLIER) cc_final: -0.1558 (mtm) REVERT: 4 134 GLU cc_start: 0.7644 (mp0) cc_final: 0.7037 (mp0) REVERT: 4 191 ILE cc_start: 0.8916 (mp) cc_final: 0.8492 (mt) REVERT: 7 205 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.4576 (mp0) outliers start: 82 outliers final: 40 residues processed: 595 average time/residue: 0.3852 time to fit residues: 345.0533 Evaluate side-chains 482 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 437 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 194 ASP Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 52 MET Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 4 residue 33 MET Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 chunk 271 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS G 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.845 24143 Z= 0.963 Angle : 0.727 30.168 32571 Z= 0.396 Chirality : 0.048 0.217 3773 Planarity : 0.005 0.061 4193 Dihedral : 6.412 86.397 3410 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.33 % Favored : 96.50 % Rotamer: Outliers : 4.34 % Allowed : 17.32 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3031 helix: 0.96 (0.14), residues: 1252 sheet: -0.41 (0.19), residues: 646 loop : -2.03 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 73 PHE 0.034 0.002 PHE 5 211 TYR 0.023 0.002 TYR G 213 ARG 0.016 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 469 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7708 (mmtp) REVERT: A 183 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 205 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7812 (m) REVERT: B 239 ARG cc_start: 0.7546 (tpt170) cc_final: 0.7238 (tpt170) REVERT: C 95 GLU cc_start: 0.8268 (tp30) cc_final: 0.7862 (tp30) REVERT: D 56 SER cc_start: 0.8069 (p) cc_final: 0.7486 (p) REVERT: D 129 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8736 (m) REVERT: E 22 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7337 (m-10) REVERT: E 222 LYS cc_start: 0.8415 (tttt) cc_final: 0.8146 (tttt) REVERT: F 121 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7939 (tm-30) REVERT: G 196 MET cc_start: 0.8283 (tpp) cc_final: 0.7876 (tpp) REVERT: G 242 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7487 (tm-30) REVERT: 1 84 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8119 (mtpp) REVERT: 2 17 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7667 (pt) REVERT: 3 106 TYR cc_start: 0.3397 (OUTLIER) cc_final: 0.2074 (t80) REVERT: 4 88 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7370 (ttm-80) REVERT: 7 44 LYS cc_start: 0.8061 (tppt) cc_final: 0.7592 (tptp) REVERT: 7 205 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5408 (mp0) outliers start: 110 outliers final: 69 residues processed: 535 average time/residue: 0.3681 time to fit residues: 302.7487 Evaluate side-chains 495 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 419 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 87 VAL Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 176 MET Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 290 optimal weight: 0.1980 chunk 143 optimal weight: 0.4980 chunk 260 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.844 24143 Z= 0.939 Angle : 0.662 30.097 32571 Z= 0.362 Chirality : 0.046 0.201 3773 Planarity : 0.004 0.051 4193 Dihedral : 6.044 87.449 3406 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 3.67 % Allowed : 19.18 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3031 helix: 1.08 (0.14), residues: 1259 sheet: -0.25 (0.19), residues: 645 loop : -1.81 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.034 0.001 PHE 5 211 TYR 0.016 0.001 TYR E 213 ARG 0.007 0.001 ARG 3 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 440 time to evaluate : 2.545 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: A 66 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7668 (mmtp) REVERT: A 143 GLU cc_start: 0.5536 (pt0) cc_final: 0.5330 (pm20) REVERT: B 70 ILE cc_start: 0.9157 (mm) cc_final: 0.8907 (mt) REVERT: B 205 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 239 ARG cc_start: 0.7544 (tpt170) cc_final: 0.7187 (tpt170) REVERT: C 95 GLU cc_start: 0.8110 (tp30) cc_final: 0.7726 (tp30) REVERT: D 56 SER cc_start: 0.7991 (p) cc_final: 0.7402 (p) REVERT: D 129 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8720 (m) REVERT: E 222 LYS cc_start: 0.8408 (tttt) cc_final: 0.8061 (tttt) REVERT: F 121 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7825 (tm-30) REVERT: G 60 GLU cc_start: 0.6965 (tt0) cc_final: 0.6731 (tt0) REVERT: 1 84 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8151 (mtpp) REVERT: 3 106 TYR cc_start: 0.3255 (OUTLIER) cc_final: 0.1777 (t80) REVERT: 3 118 GLU cc_start: 0.7181 (pp20) cc_final: 0.6969 (pp20) REVERT: 3 134 GLU cc_start: 0.6774 (mp0) cc_final: 0.6168 (mt-10) REVERT: 3 138 VAL cc_start: 0.8806 (p) cc_final: 0.8580 (p) REVERT: 4 88 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7328 (ttm-80) REVERT: 4 191 ILE cc_start: 0.8834 (mp) cc_final: 0.8529 (mt) REVERT: 5 51 ARG cc_start: 0.7495 (mmp80) cc_final: 0.7286 (mmt180) REVERT: 5 110 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8572 (mt) REVERT: 6 163 GLU cc_start: 0.6050 (tp30) cc_final: 0.5801 (tp30) REVERT: 7 44 LYS cc_start: 0.8123 (tppt) cc_final: 0.7609 (tptp) REVERT: 7 205 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5458 (mp0) outliers start: 93 outliers final: 58 residues processed: 499 average time/residue: 0.3669 time to fit residues: 281.6052 Evaluate side-chains 462 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 399 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 5 residue 154 ARG Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 248 optimal weight: 0.0870 chunk 201 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN 3 35 ASN 5 198 GLN 7 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.847 24143 Z= 0.957 Angle : 0.672 29.975 32571 Z= 0.366 Chirality : 0.046 0.181 3773 Planarity : 0.004 0.047 4193 Dihedral : 5.847 86.415 3404 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 3.99 % Allowed : 19.73 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3031 helix: 1.04 (0.14), residues: 1254 sheet: -0.26 (0.19), residues: 655 loop : -1.69 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.035 0.002 PHE 5 211 TYR 0.018 0.001 TYR E 213 ARG 0.006 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 428 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7890 (t0) REVERT: B 205 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7762 (m) REVERT: B 239 ARG cc_start: 0.7587 (tpt170) cc_final: 0.7156 (tpt170) REVERT: C 95 GLU cc_start: 0.8129 (tp30) cc_final: 0.7736 (tp30) REVERT: D 56 SER cc_start: 0.8112 (p) cc_final: 0.7879 (p) REVERT: E 222 LYS cc_start: 0.8478 (tttt) cc_final: 0.8081 (tttt) REVERT: F 121 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7857 (tm-30) REVERT: F 234 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: G 60 GLU cc_start: 0.7071 (tt0) cc_final: 0.6730 (tt0) REVERT: 1 84 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8080 (mtpp) REVERT: 1 134 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: 3 51 ARG cc_start: 0.7972 (mmp80) cc_final: 0.7711 (mmp80) REVERT: 3 106 TYR cc_start: 0.3275 (OUTLIER) cc_final: 0.1626 (t80) REVERT: 3 118 GLU cc_start: 0.7307 (pp20) cc_final: 0.6991 (pp20) REVERT: 5 110 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8652 (mt) REVERT: 6 88 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7538 (ttp-110) REVERT: 6 152 GLU cc_start: 0.6165 (mt-10) cc_final: 0.5822 (mt-10) REVERT: 7 44 LYS cc_start: 0.8388 (tppt) cc_final: 0.7969 (tptp) REVERT: 7 205 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5526 (mp0) outliers start: 101 outliers final: 75 residues processed: 493 average time/residue: 0.3648 time to fit residues: 275.6929 Evaluate side-chains 494 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 412 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 3 residue 200 SER Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 97 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 170 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 291 optimal weight: 0.6980 chunk 241 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 152 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN E 125 GLN 4 96 ASN 4 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.848 24143 Z= 0.943 Angle : 0.642 29.893 32571 Z= 0.350 Chirality : 0.046 0.189 3773 Planarity : 0.004 0.045 4193 Dihedral : 5.656 85.608 3404 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 4.06 % Allowed : 20.99 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3031 helix: 1.14 (0.15), residues: 1254 sheet: -0.25 (0.19), residues: 654 loop : -1.63 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 73 PHE 0.035 0.001 PHE 5 211 TYR 0.016 0.001 TYR E 213 ARG 0.008 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 427 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.8787 (m-80) cc_final: 0.8495 (m-80) REVERT: B 104 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7526 (t0) REVERT: B 186 ASP cc_start: 0.7119 (t0) cc_final: 0.6797 (t0) REVERT: B 205 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7801 (m) REVERT: C 95 GLU cc_start: 0.8100 (tp30) cc_final: 0.7731 (tp30) REVERT: E 222 LYS cc_start: 0.8514 (tttt) cc_final: 0.8269 (tttt) REVERT: F 121 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 234 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: G 208 ASN cc_start: 0.7493 (p0) cc_final: 0.6790 (p0) REVERT: 1 84 LYS cc_start: 0.8257 (ttmm) cc_final: 0.8034 (mtpp) REVERT: 1 134 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: 2 121 SER cc_start: 0.8799 (p) cc_final: 0.8591 (p) REVERT: 3 106 TYR cc_start: 0.3102 (OUTLIER) cc_final: 0.1181 (t80) REVERT: 4 29 LYS cc_start: 0.7410 (ttmt) cc_final: 0.7091 (ttmm) REVERT: 5 110 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8654 (mt) REVERT: 7 44 LYS cc_start: 0.8012 (tppt) cc_final: 0.7596 (tptp) REVERT: 7 51 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7531 (mmt-90) REVERT: 7 83 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7153 (ptp-170) REVERT: 7 205 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5460 (mp0) outliers start: 103 outliers final: 76 residues processed: 487 average time/residue: 0.3670 time to fit residues: 273.6541 Evaluate side-chains 498 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 414 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 83 ARG Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 280 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 chunk 165 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 245 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.850 24143 Z= 0.953 Angle : 0.658 29.909 32571 Z= 0.357 Chirality : 0.047 0.256 3773 Planarity : 0.004 0.047 4193 Dihedral : 5.632 84.696 3404 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 4.34 % Allowed : 21.23 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3031 helix: 1.12 (0.15), residues: 1246 sheet: -0.25 (0.19), residues: 649 loop : -1.60 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 73 PHE 0.035 0.001 PHE 5 211 TYR 0.017 0.001 TYR E 213 ARG 0.011 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 424 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.8828 (m-80) cc_final: 0.8571 (m-80) REVERT: A 196 MET cc_start: 0.8409 (mmm) cc_final: 0.8137 (tpp) REVERT: B 104 ASP cc_start: 0.8079 (t0) cc_final: 0.7557 (t0) REVERT: B 186 ASP cc_start: 0.7126 (t0) cc_final: 0.6806 (t0) REVERT: B 205 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7828 (m) REVERT: C 95 GLU cc_start: 0.8106 (tp30) cc_final: 0.7699 (tp30) REVERT: E 222 LYS cc_start: 0.8514 (tttt) cc_final: 0.8224 (tttt) REVERT: F 121 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7777 (tm-30) REVERT: G 208 ASN cc_start: 0.7551 (p0) cc_final: 0.6976 (p0) REVERT: 1 83 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8225 (ttp80) REVERT: 1 134 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: 2 121 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8787 (p) REVERT: 3 106 TYR cc_start: 0.3069 (OUTLIER) cc_final: 0.0928 (t80) REVERT: 3 118 GLU cc_start: 0.7386 (pp20) cc_final: 0.7010 (pp20) REVERT: 4 29 LYS cc_start: 0.7342 (ttmt) cc_final: 0.7073 (ttmm) REVERT: 5 55 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7531 (p) REVERT: 5 110 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8664 (mt) REVERT: 7 44 LYS cc_start: 0.8299 (tppt) cc_final: 0.7848 (tptp) REVERT: 7 51 ARG cc_start: 0.8214 (mmt-90) cc_final: 0.7649 (mmt180) REVERT: 7 187 ASP cc_start: 0.6898 (p0) cc_final: 0.6647 (p0) REVERT: 7 205 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5327 (mp0) outliers start: 110 outliers final: 87 residues processed: 498 average time/residue: 0.3758 time to fit residues: 290.1339 Evaluate side-chains 513 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 419 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 1 residue 193 GLU Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 110 LEU Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 136 ASP Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 173 optimal weight: 0.0030 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 197 optimal weight: 0.0170 chunk 143 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.854 24143 Z= 0.941 Angle : 0.632 29.843 32571 Z= 0.343 Chirality : 0.046 0.209 3773 Planarity : 0.004 0.063 4193 Dihedral : 5.494 83.364 3404 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 3.83 % Allowed : 22.10 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3031 helix: 1.20 (0.15), residues: 1249 sheet: -0.19 (0.19), residues: 646 loop : -1.54 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 73 PHE 0.035 0.001 PHE 5 211 TYR 0.015 0.001 TYR E 213 ARG 0.016 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 441 time to evaluate : 2.402 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: A 159 TYR cc_start: 0.8789 (m-80) cc_final: 0.8509 (m-80) REVERT: B 104 ASP cc_start: 0.7974 (t0) cc_final: 0.7446 (t0) REVERT: B 186 ASP cc_start: 0.7109 (t0) cc_final: 0.6781 (t0) REVERT: B 205 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7740 (m) REVERT: C 21 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8977 (mp) REVERT: C 95 GLU cc_start: 0.8084 (tp30) cc_final: 0.7693 (tp30) REVERT: F 121 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7707 (tm-30) REVERT: G 102 THR cc_start: 0.9368 (p) cc_final: 0.9107 (m) REVERT: G 208 ASN cc_start: 0.7432 (p0) cc_final: 0.6924 (p0) REVERT: 2 120 LYS cc_start: 0.7880 (mptt) cc_final: 0.7390 (mptt) REVERT: 2 121 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8770 (p) REVERT: 3 106 TYR cc_start: 0.3514 (OUTLIER) cc_final: 0.1458 (t80) REVERT: 4 29 LYS cc_start: 0.7268 (ttmt) cc_final: 0.7021 (ttmm) REVERT: 5 25 MET cc_start: 0.7896 (ttm) cc_final: 0.7616 (ttp) REVERT: 5 55 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7376 (p) REVERT: 7 44 LYS cc_start: 0.7980 (tppt) cc_final: 0.7566 (tptp) REVERT: 7 51 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7607 (mmt180) REVERT: 7 83 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7087 (ptp-170) REVERT: 7 205 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5346 (mp0) outliers start: 97 outliers final: 76 residues processed: 508 average time/residue: 0.3558 time to fit residues: 279.2012 Evaluate side-chains 516 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 433 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 182 SER Chi-restraints excluded: chain 1 residue 193 GLU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 121 SER Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 6 residue 161 VAL Chi-restraints excluded: chain 7 residue 83 ARG Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 195 GLU Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 270 optimal weight: 0.2980 chunk 162 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 269 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.861 24143 Z= 0.958 Angle : 0.660 29.709 32571 Z= 0.356 Chirality : 0.046 0.199 3773 Planarity : 0.004 0.084 4193 Dihedral : 5.480 82.250 3400 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 3.79 % Allowed : 22.38 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3031 helix: 1.13 (0.14), residues: 1252 sheet: -0.19 (0.19), residues: 650 loop : -1.50 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 73 PHE 0.035 0.001 PHE 5 211 TYR 0.017 0.001 TYR E 213 ARG 0.023 0.001 ARG 5 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 431 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7780 (mmtp) REVERT: A 159 TYR cc_start: 0.8815 (m-80) cc_final: 0.8538 (m-80) REVERT: A 196 MET cc_start: 0.8427 (mmm) cc_final: 0.8162 (tpp) REVERT: B 104 ASP cc_start: 0.8089 (t0) cc_final: 0.7552 (t0) REVERT: B 186 ASP cc_start: 0.7087 (t0) cc_final: 0.6742 (t0) REVERT: B 205 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7777 (m) REVERT: C 95 GLU cc_start: 0.8107 (tp30) cc_final: 0.7708 (tp30) REVERT: F 121 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7751 (tm-30) REVERT: G 208 ASN cc_start: 0.7427 (p0) cc_final: 0.6942 (p0) REVERT: 2 120 LYS cc_start: 0.7946 (mptt) cc_final: 0.7484 (mptt) REVERT: 3 106 TYR cc_start: 0.3587 (OUTLIER) cc_final: 0.1437 (t80) REVERT: 4 29 LYS cc_start: 0.7362 (ttmt) cc_final: 0.7111 (ttmm) REVERT: 5 51 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7384 (mmp80) REVERT: 5 55 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7208 (p) REVERT: 7 44 LYS cc_start: 0.8036 (tppt) cc_final: 0.7673 (tptp) REVERT: 7 51 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7678 (mmt180) REVERT: 7 83 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7079 (ptp-170) REVERT: 7 187 ASP cc_start: 0.6965 (p0) cc_final: 0.6674 (p0) REVERT: 7 205 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5374 (mp0) outliers start: 96 outliers final: 75 residues processed: 497 average time/residue: 0.3672 time to fit residues: 281.7302 Evaluate side-chains 493 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 413 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 156 THR Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 193 GLU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 83 ARG Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 0.4980 chunk 285 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 299 optimal weight: 0.3980 chunk 275 optimal weight: 0.0000 chunk 238 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.869 24143 Z= 0.942 Angle : 0.639 29.550 32571 Z= 0.345 Chirality : 0.045 0.198 3773 Planarity : 0.004 0.108 4193 Dihedral : 5.385 81.180 3400 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 3.28 % Allowed : 22.69 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3031 helix: 1.22 (0.14), residues: 1260 sheet: -0.15 (0.19), residues: 634 loop : -1.50 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 73 PHE 0.033 0.001 PHE 5 211 TYR 0.014 0.001 TYR E 213 ARG 0.029 0.001 ARG 5 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 423 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7770 (mmtp) REVERT: A 159 TYR cc_start: 0.8741 (m-80) cc_final: 0.8477 (m-80) REVERT: B 104 ASP cc_start: 0.7952 (t0) cc_final: 0.7397 (t0) REVERT: B 186 ASP cc_start: 0.7094 (t0) cc_final: 0.6749 (t0) REVERT: B 205 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7745 (m) REVERT: C 95 GLU cc_start: 0.8060 (tp30) cc_final: 0.7686 (tp30) REVERT: F 121 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7700 (tm-30) REVERT: G 104 ASP cc_start: 0.7679 (t70) cc_final: 0.6933 (t0) REVERT: G 208 ASN cc_start: 0.7278 (p0) cc_final: 0.6857 (p0) REVERT: 2 120 LYS cc_start: 0.7780 (mptt) cc_final: 0.7466 (mptt) REVERT: 3 106 TYR cc_start: 0.3551 (OUTLIER) cc_final: 0.1380 (t80) REVERT: 3 118 GLU cc_start: 0.7288 (pp20) cc_final: 0.6785 (pp20) REVERT: 5 25 MET cc_start: 0.7908 (ttm) cc_final: 0.7639 (ttp) REVERT: 7 44 LYS cc_start: 0.8003 (tppt) cc_final: 0.7645 (tptp) REVERT: 7 51 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7615 (mmt180) REVERT: 7 83 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7013 (ptp-170) REVERT: 7 205 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5354 (mp0) outliers start: 83 outliers final: 75 residues processed: 478 average time/residue: 0.3583 time to fit residues: 264.4851 Evaluate side-chains 489 residues out of total 2534 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 410 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 117 CYS Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 87 VAL Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 161 VAL Chi-restraints excluded: chain 1 residue 170 ARG Chi-restraints excluded: chain 1 residue 193 GLU Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 60 VAL Chi-restraints excluded: chain 2 residue 75 ASN Chi-restraints excluded: chain 2 residue 186 ILE Chi-restraints excluded: chain 2 residue 187 ASP Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 106 TYR Chi-restraints excluded: chain 3 residue 161 VAL Chi-restraints excluded: chain 4 residue 87 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 136 ASP Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 54 MET Chi-restraints excluded: chain 6 residue 148 TYR Chi-restraints excluded: chain 6 residue 156 THR Chi-restraints excluded: chain 7 residue 83 ARG Chi-restraints excluded: chain 7 residue 121 SER Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 205 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 0.1980 chunk 254 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 239 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 245 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 44 optimal weight: 0.0870 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.186762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.144156 restraints weight = 25773.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149322 restraints weight = 15870.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.152667 restraints weight = 11669.101| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.878 24143 Z= 0.937 Angle : 0.627 29.346 32571 Z= 0.339 Chirality : 0.045 0.204 3773 Planarity : 0.004 0.133 4193 Dihedral : 5.281 80.251 3400 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 3.04 % Allowed : 23.32 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3031 helix: 1.36 (0.14), residues: 1265 sheet: -0.12 (0.19), residues: 636 loop : -1.43 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 73 PHE 0.029 0.001 PHE 5 211 TYR 0.013 0.001 TYR E 213 ARG 0.035 0.001 ARG 5 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5665.15 seconds wall clock time: 101 minutes 47.97 seconds (6107.97 seconds total)