Starting phenix.real_space_refine on Mon Sep 30 02:37:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/09_2024/6he5_0210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/09_2024/6he5_0210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/09_2024/6he5_0210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/09_2024/6he5_0210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/09_2024/6he5_0210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he5_0210/09_2024/6he5_0210.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 15633 2.51 5 N 4127 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 412 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24633 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "C" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "D" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "F" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "G" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1907 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain: "1" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "3" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "4" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "5" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "6" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 195} Chain: "7" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1552 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'TRANS': 6} Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'TRANS': 7} Time building chain proxies: 15.16, per 1000 atoms: 0.62 Number of scatterers: 24633 At special positions: 0 Unit cell: (131.32, 134, 108.54, 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 97 16.00 O 4776 8.00 N 4127 7.00 C 15633 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: 6.19 Conformation dependent library (CDL) restraints added in 3.2 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 33 sheets defined 40.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.806A pdb=" N LYS A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 34' Processing helix chain 'A' and resid 81 through 103 removed outlier: 3.844A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.561A pdb=" N LYS A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.801A pdb=" N GLU A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.518A pdb=" N ILE A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 225 through 244 removed outlier: 3.651A pdb=" N LYS A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.710A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.513A pdb=" N VAL B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 removed outlier: 3.790A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.631A pdb=" N TYR B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.584A pdb=" N GLU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 201 Processing helix chain 'B' and resid 225 through 245 Proline residue: B 231 - end of helix removed outlier: 4.066A pdb=" N GLU B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 81 through 103 removed outlier: 3.916A pdb=" N VAL C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.836A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 201 Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.762A pdb=" N LYS C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Proline residue: C 231 - end of helix removed outlier: 3.638A pdb=" N ARG C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.557A 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 103 removed outlier: 3.866A pdb=" N VAL D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.588A pdb=" N GLU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 225 through 243 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: 4.615A pdb=" N GLU D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.573A pdb=" N ARG E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.578A pdb=" N ARG E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.717A pdb=" N TYR E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.969A pdb=" N LYS E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 201 removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.627A pdb=" N GLU E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.877A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 104 removed outlier: 3.747A pdb=" N ARG F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.574A pdb=" N TYR F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 Processing helix chain 'F' and resid 184 through 201 Processing helix chain 'F' and resid 225 through 244 removed outlier: 3.597A pdb=" N LYS F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Proline residue: F 231 - end of helix removed outlier: 4.106A pdb=" N GLU F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG F 239 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.781A pdb=" N GLU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 104 removed outlier: 3.889A pdb=" N VAL G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.758A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.843A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 229 through 246 removed outlier: 4.077A pdb=" N GLU G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG G 239 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain '1' and resid 59 through 82 removed outlier: 3.603A pdb=" N PHE 1 65 " --> pdb=" O GLY 1 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE 1 69 " --> pdb=" O PHE 1 65 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 101 removed outlier: 3.753A pdb=" N ILE 1 90 " --> pdb=" O THR 1 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER 1 95 " --> pdb=" O ALA 1 91 " (cutoff:3.500A) Processing helix chain '1' and resid 143 through 153 removed outlier: 4.660A pdb=" N GLY 1 149 " --> pdb=" O LEU 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 179 removed outlier: 3.608A pdb=" N GLU 1 166 " --> pdb=" O ASP 1 162 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP 1 179 " --> pdb=" O ALA 1 175 " (cutoff:3.500A) Processing helix chain '1' and resid 199 through 208 removed outlier: 4.326A pdb=" N GLU 1 203 " --> pdb=" O TYR 1 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN 1 206 " --> pdb=" O GLU 1 202 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE 1 207 " --> pdb=" O GLU 1 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 1 208 " --> pdb=" O VAL 1 204 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 82 removed outlier: 3.711A pdb=" N ARG 2 68 " --> pdb=" O GLN 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 101 removed outlier: 3.669A pdb=" N ILE 2 90 " --> pdb=" O THR 2 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 2 96 " --> pdb=" O THR 2 92 " (cutoff:3.500A) Processing helix chain '2' and resid 143 through 153 removed outlier: 3.596A pdb=" N ASP 2 153 " --> pdb=" O GLY 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 163 through 177 removed outlier: 3.950A pdb=" N LEU 2 167 " --> pdb=" O GLU 2 163 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS 2 177 " --> pdb=" O TYR 2 173 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 206 removed outlier: 4.225A pdb=" N GLU 2 203 " --> pdb=" O TYR 2 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 2 204 " --> pdb=" O SER 2 200 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN 2 206 " --> pdb=" O GLU 2 202 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 82 removed outlier: 3.616A pdb=" N ALA 3 63 " --> pdb=" O SER 3 59 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE 3 69 " --> pdb=" O PHE 3 65 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 3 70 " --> pdb=" O LEU 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 101 Processing helix chain '3' and resid 143 through 154 removed outlier: 4.111A pdb=" N GLY 3 149 " --> pdb=" O LEU 3 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 3 150 " --> pdb=" O THR 3 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP 3 153 " --> pdb=" O GLY 3 149 " (cutoff:3.500A) Processing helix chain '3' and resid 160 through 176 removed outlier: 3.560A pdb=" N GLU 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA 3 175 " --> pdb=" O ALA 3 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET 3 176 " --> pdb=" O ILE 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 200 through 206 Processing helix chain '4' and resid 59 through 82 removed outlier: 3.709A pdb=" N ILE 4 69 " --> pdb=" O PHE 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 86 through 101 Processing helix chain '4' and resid 143 through 154 removed outlier: 3.790A pdb=" N VAL 4 150 " --> pdb=" O THR 4 146 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP 4 153 " --> pdb=" O GLY 4 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 4 154 " --> pdb=" O VAL 4 150 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 removed outlier: 3.885A pdb=" N GLU 4 166 " --> pdb=" O ASP 4 162 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 4 175 " --> pdb=" O ALA 4 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS 4 177 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 199 through 209 removed outlier: 3.924A pdb=" N GLU 4 203 " --> pdb=" O TYR 4 199 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE 4 207 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 82 removed outlier: 3.605A pdb=" N ALA 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE 5 65 " --> pdb=" O GLY 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 101 Processing helix chain '5' and resid 143 through 152 removed outlier: 3.559A pdb=" N GLU 5 152 " --> pdb=" O TYR 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 removed outlier: 3.908A pdb=" N GLU 5 166 " --> pdb=" O ASP 5 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER 5 174 " --> pdb=" O ARG 5 170 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA 5 175 " --> pdb=" O ALA 5 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET 5 176 " --> pdb=" O ILE 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 179 through 184 removed outlier: 3.781A pdb=" N SER 5 182 " --> pdb=" O ASP 5 179 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP 5 184 " --> pdb=" O ALA 5 181 " (cutoff:3.500A) Processing helix chain '5' and resid 199 through 206 removed outlier: 4.443A pdb=" N GLU 5 203 " --> pdb=" O TYR 5 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL 5 204 " --> pdb=" O SER 5 200 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 82 removed outlier: 3.732A pdb=" N ILE 6 69 " --> pdb=" O PHE 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 101 removed outlier: 3.511A pdb=" N ILE 6 90 " --> pdb=" O THR 6 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 6 100 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR 6 101 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 155 removed outlier: 3.630A pdb=" N GLY 6 149 " --> pdb=" O LEU 6 145 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 179 removed outlier: 3.506A pdb=" N ALA 6 164 " --> pdb=" O GLY 6 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 6 166 " --> pdb=" O ASP 6 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE 6 172 " --> pdb=" O ALA 6 168 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS 6 177 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 208 removed outlier: 4.122A pdb=" N GLU 6 203 " --> pdb=" O TYR 6 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 6 204 " --> pdb=" O SER 6 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN 6 206 " --> pdb=" O GLU 6 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 6 207 " --> pdb=" O GLU 6 203 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 82 Processing helix chain '7' and resid 86 through 101 Processing helix chain '7' and resid 143 through 154 removed outlier: 3.800A pdb=" N GLY 7 149 " --> pdb=" O LEU 7 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 7 150 " --> pdb=" O THR 7 146 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP 7 153 " --> pdb=" O GLY 7 149 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 154 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 163 through 177 removed outlier: 3.837A pdb=" N LEU 7 167 " --> pdb=" O GLU 7 163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG 7 170 " --> pdb=" O GLU 7 166 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS 7 177 " --> pdb=" O TYR 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 199 through 205 removed outlier: 4.392A pdb=" N GLU 7 203 " --> pdb=" O TYR 7 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 7 204 " --> pdb=" O SER 7 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.659A pdb=" N VAL A 211 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.698A pdb=" N LEU A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 147 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.575A pdb=" N GLY B 45 " --> pdb=" O CYS B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.219A pdb=" N ILE B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 147 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.836A 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: 4.152A pdb=" N LEU C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 147 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.150A pdb=" N LEU D 147 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.522A pdb=" N GLY E 45 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL E 211 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 215 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.553A pdb=" N ALA E 77 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.524A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL F 211 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.565A pdb=" N LEU F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 147 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 69 removed outlier: 4.857A pdb=" N GLY F 80 " --> pdb=" O VAL M 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.521A pdb=" N ALA G 37 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AB7, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.508A pdb=" N VAL L 398 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain '1' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain '1' and resid 45 through 49 removed outlier: 6.700A pdb=" N MET 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 125 " --> pdb=" O LEU 1 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY 1 114 " --> pdb=" O SER 1 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER 1 121 " --> pdb=" O GLY 1 114 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 137 through 138 removed outlier: 3.651A pdb=" N ASP 2 187 " --> pdb=" O THR 2 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '2' and resid 32 through 33 Processing sheet with id=AC4, first strand: chain '2' and resid 45 through 49 removed outlier: 6.609A pdb=" N MET 2 52 " --> pdb=" O ILE 2 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 2 110 " --> pdb=" O ILE 2 125 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE 2 122 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 14 through 18 removed outlier: 3.540A pdb=" N ALA 3 26 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET 3 25 " --> pdb=" O VAL 3 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP 3 187 " --> pdb=" O THR 3 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 46 through 49 removed outlier: 6.667A pdb=" N MET 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 137 through 138 removed outlier: 4.020A pdb=" N VAL 4 138 " --> pdb=" O GLY 4 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY 4 16 " --> pdb=" O VAL 4 138 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL 4 15 " --> pdb=" O ALA 4 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 46 through 49 removed outlier: 6.555A pdb=" N MET 4 52 " --> pdb=" O ILE 4 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 137 through 140 removed outlier: 3.637A pdb=" N ILE 5 191 " --> pdb=" O VAL 5 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 45 through 49 removed outlier: 6.742A pdb=" N MET 5 52 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 5 121 " --> pdb=" O GLY 5 114 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE 5 122 " --> pdb=" O GLU 5 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 5 132 " --> pdb=" O SER 5 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 14 through 18 removed outlier: 3.722A pdb=" N TYR 6 197 " --> pdb=" O LYS 6 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 31 through 33 removed outlier: 6.738A pdb=" N ALA 6 31 " --> pdb=" O ALA 6 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 45 through 49 removed outlier: 6.824A pdb=" N ILE 6 45 " --> pdb=" O THR 6 56 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR 6 56 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN 6 47 " --> pdb=" O MET 6 54 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET 6 54 " --> pdb=" O GLN 6 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY 6 113 " --> pdb=" O ALA 6 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 6 110 " --> pdb=" O ILE 6 125 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 137 through 141 removed outlier: 5.394A pdb=" N THR 7 13 " --> pdb=" O GLU 7 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU 7 28 " --> pdb=" O THR 7 13 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 7 22 " --> pdb=" O CYS 7 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 7 23 " --> pdb=" O ILE 7 191 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE 7 122 " --> pdb=" O GLU 7 134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 7 132 " --> pdb=" O SER 7 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP 7 126 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3699 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: 9.35 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.23: 1776 1.23 - 1.46: 10918 1.46 - 1.69: 12100 1.69 - 1.92: 167 1.92 - 2.15: 7 Bond restraints: 24968 Sorted by residual: bond pdb=" CZ ARG 5 170 " pdb=" NH2 ARG 5 170 " ideal model delta sigma weight residual 1.330 2.147 -0.817 1.30e-02 5.92e+03 3.95e+03 bond pdb=" CG PHE 5 211 " pdb=" CD1 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.104 -0.720 2.10e-02 2.27e+03 1.17e+03 bond pdb=" CG PHE 5 211 " pdb=" CD2 PHE 5 211 " ideal model delta sigma weight residual 1.384 2.041 -0.657 2.10e-02 2.27e+03 9.80e+02 bond pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 1.330 1.710 -0.380 1.23e-02 6.61e+03 9.52e+02 bond pdb=" N GLN E 5 " pdb=" CA GLN E 5 " ideal model delta sigma weight residual 1.458 1.000 0.458 1.90e-02 2.77e+03 5.80e+02 ... (remaining 24963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 26571 4.27 - 8.54: 6410 8.54 - 12.81: 642 12.81 - 17.07: 33 17.07 - 21.34: 4 Bond angle restraints: 33660 Sorted by residual: angle pdb=" NE ARG 5 170 " pdb=" CZ ARG 5 170 " pdb=" NH1 ARG 5 170 " ideal model delta sigma weight residual 121.50 101.39 20.11 1.00e+00 1.00e+00 4.05e+02 angle pdb=" N LYS 2 40 " pdb=" CA LYS 2 40 " pdb=" C LYS 2 40 " ideal model delta sigma weight residual 114.62 95.87 18.75 1.14e+00 7.69e-01 2.71e+02 angle pdb=" C GLU E 65 " pdb=" N LYS E 66 " pdb=" CA LYS E 66 " ideal model delta sigma weight residual 120.38 141.72 -21.34 1.37e+00 5.33e-01 2.43e+02 angle pdb=" CA LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 117.22 101.99 15.23 1.17e+00 7.31e-01 1.69e+02 angle pdb=" O LYS E 66 " pdb=" C LYS E 66 " pdb=" N ILE E 67 " ideal model delta sigma weight residual 122.12 135.88 -13.76 1.06e+00 8.90e-01 1.69e+02 ... (remaining 33655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14375 25.08 - 50.16: 682 50.16 - 75.23: 224 75.23 - 100.31: 60 100.31 - 125.39: 2 Dihedral angle restraints: 15343 sinusoidal: 6204 harmonic: 9139 Sorted by residual: dihedral pdb=" CA GLU A 65 " pdb=" C GLU A 65 " pdb=" N LYS A 66 " pdb=" CA LYS A 66 " ideal model delta harmonic sigma weight residual -180.00 -54.61 -125.39 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA GLY H 394 " pdb=" C GLY H 394 " pdb=" N VAL H 395 " pdb=" CA VAL H 395 " ideal model delta harmonic sigma weight residual -180.00 -70.34 -109.66 0 5.00e+00 4.00e-02 4.81e+02 dihedral pdb=" CA ALA 2 139 " pdb=" C ALA 2 139 " pdb=" N THR 2 140 " pdb=" CA THR 2 140 " ideal model delta harmonic sigma weight residual 180.00 110.18 69.82 0 5.00e+00 4.00e-02 1.95e+02 ... (remaining 15340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 2874 0.225 - 0.450: 890 0.450 - 0.674: 107 0.674 - 0.899: 9 0.899 - 1.124: 1 Chirality restraints: 3881 Sorted by residual: chirality pdb=" CA THR 3 140 " pdb=" N THR 3 140 " pdb=" C THR 3 140 " pdb=" CB THR 3 140 " both_signs ideal model delta sigma weight residual False 2.53 1.40 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASP B 217 " pdb=" N ASP B 217 " pdb=" C ASP B 217 " pdb=" CB ASP B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA GLU D 65 " pdb=" N GLU D 65 " pdb=" C GLU D 65 " pdb=" CB GLU D 65 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3878 not shown) Planarity restraints: 4329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 5 199 " 0.225 2.00e-02 2.50e+03 1.45e-01 4.21e+02 pdb=" CG TYR 5 199 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR 5 199 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR 5 199 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 TYR 5 199 " -0.166 2.00e-02 2.50e+03 pdb=" CE2 TYR 5 199 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR 5 199 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR 5 199 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 123 " 0.214 2.00e-02 2.50e+03 1.28e-01 3.30e+02 pdb=" CG TYR G 123 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 123 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 TYR G 123 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR G 123 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR G 123 " -0.121 2.00e-02 2.50e+03 pdb=" CZ TYR G 123 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR G 123 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 101 " -0.196 2.00e-02 2.50e+03 1.26e-01 3.20e+02 pdb=" CG TYR 3 101 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 101 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 101 " 0.142 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 101 " 0.139 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 101 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR 3 101 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR 3 101 " -0.209 2.00e-02 2.50e+03 ... (remaining 4326 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3223 2.77 - 3.30: 22758 3.30 - 3.83: 39960 3.83 - 4.37: 53183 4.37 - 4.90: 84967 Nonbonded interactions: 204091 Sorted by model distance: nonbonded pdb=" NH2 ARG 5 170 " pdb=" CD2 PHE 5 211 " model vdw 2.236 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CG PHE 5 211 " model vdw 2.237 3.340 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE1 PHE 5 211 " model vdw 2.242 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CE2 PHE 5 211 " model vdw 2.250 3.420 nonbonded pdb=" NH2 ARG 5 170 " pdb=" CZ PHE 5 211 " model vdw 2.251 3.420 ... (remaining 204086 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 3.010 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: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.310 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 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 : 0.036 0.817 24968 Z= 2.339 Angle : 3.508 21.343 33660 Z= 2.349 Chirality : 0.204 1.124 3881 Planarity : 0.030 0.297 4329 Dihedral : 17.648 125.386 9493 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 2.18 % Allowed : 5.32 % Favored : 92.50 % Rotamer: Outliers : 4.51 % Allowed : 9.74 % Favored : 85.75 % Cbeta Deviations : 6.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 1.10 % Twisted General : 0.82 % 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: -2.68 (0.13), residues: 3122 helix: -1.29 (0.13), residues: 1197 sheet: -0.43 (0.20), residues: 563 loop : -2.82 (0.13), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.032 0.015 HIS G 73 PHE 0.189 0.040 PHE A 221 TYR 0.243 0.049 TYR F 8 ARG 0.091 0.012 ARG 1 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1303 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6469 (mm-30) REVERT: A 208 ASN cc_start: 0.7788 (p0) cc_final: 0.7355 (p0) REVERT: A 211 VAL cc_start: 0.7891 (t) cc_final: 0.7541 (p) REVERT: A 220 THR cc_start: 0.8239 (m) cc_final: 0.8001 (m) REVERT: B 24 VAL cc_start: 0.8283 (t) cc_final: 0.7918 (t) REVERT: B 152 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8594 (Cg_endo) REVERT: B 208 ASN cc_start: 0.6638 (p0) cc_final: 0.6217 (p0) REVERT: C 23 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8165 (tp40) REVERT: C 41 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8068 (ttpt) REVERT: C 47 ILE cc_start: 0.8472 (mt) cc_final: 0.8268 (mt) REVERT: C 66 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8238 (tppt) REVERT: C 144 VAL cc_start: 0.8745 (m) cc_final: 0.8487 (m) REVERT: C 160 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7672 (mtpt) REVERT: D 82 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8625 (t) REVERT: D 89 ILE cc_start: 0.9190 (tp) cc_final: 0.8989 (tp) REVERT: D 115 LYS cc_start: 0.8472 (mttm) cc_final: 0.7842 (mttt) REVERT: D 121 GLN cc_start: 0.8060 (tm130) cc_final: 0.7739 (tm130) REVERT: D 174 PHE cc_start: 0.7339 (t80) cc_final: 0.6543 (t80) REVERT: D 211 VAL cc_start: 0.8980 (t) cc_final: 0.8740 (t) REVERT: E 25 GLU cc_start: 0.6352 (tp30) cc_final: 0.5641 (tp30) REVERT: E 41 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7080 (ptmt) REVERT: E 49 ILE cc_start: 0.6840 (tt) cc_final: 0.6612 (tt) REVERT: E 68 TYR cc_start: 0.8023 (m-80) cc_final: 0.7711 (m-80) REVERT: E 116 ILE cc_start: 0.8525 (mt) cc_final: 0.8311 (mt) REVERT: E 120 LYS cc_start: 0.7119 (mttt) cc_final: 0.6897 (mttm) REVERT: E 186 ASP cc_start: 0.6779 (m-30) cc_final: 0.6126 (m-30) REVERT: E 235 ARG cc_start: 0.6204 (ttp-170) cc_final: 0.5559 (ttp80) REVERT: F 22 PHE cc_start: 0.6992 (m-80) cc_final: 0.6426 (m-80) REVERT: F 99 ASN cc_start: 0.7781 (t0) cc_final: 0.7479 (t0) REVERT: F 106 PRO cc_start: 0.9192 (Cg_exo) cc_final: 0.8719 (Cg_endo) REVERT: G 5 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.3614 (pm20) REVERT: G 16 SER cc_start: 0.7584 (p) cc_final: 0.7164 (p) REVERT: G 23 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7965 (tp40) REVERT: G 47 ILE cc_start: 0.8519 (mt) cc_final: 0.7807 (mt) REVERT: G 157 LEU cc_start: 0.7984 (mt) cc_final: 0.7609 (mt) REVERT: G 171 VAL cc_start: 0.5969 (t) cc_final: 0.4258 (t) REVERT: G 200 ILE cc_start: 0.7751 (pt) cc_final: 0.7388 (pt) REVERT: G 224 VAL cc_start: 0.6674 (t) cc_final: 0.6304 (t) REVERT: 1 107 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0710 (pt) REVERT: 2 44 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3402 (mptm) REVERT: 2 162 ASP cc_start: 0.4157 (m-30) cc_final: 0.3663 (m-30) REVERT: 3 46 TYR cc_start: 0.7226 (m-80) cc_final: 0.6548 (m-80) REVERT: 3 93 LEU cc_start: 0.8152 (tp) cc_final: 0.7541 (tt) REVERT: 4 70 ILE cc_start: 0.9169 (mt) cc_final: 0.8903 (mt) REVERT: 5 146 THR cc_start: 0.6265 (p) cc_final: 0.5914 (p) REVERT: 6 155 PHE cc_start: 0.3192 (t80) cc_final: 0.2981 (t80) outliers start: 118 outliers final: 19 residues processed: 1361 average time/residue: 0.4175 time to fit residues: 835.4649 Evaluate side-chains 1112 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1088 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 237 ASN G 97 GLN G 99 ASN 1 64 GLN 3 96 ASN 4 99 ASN 7 109 GLN 7 198 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 24968 Z= 0.342 Angle : 0.872 14.225 33660 Z= 0.478 Chirality : 0.052 0.223 3881 Planarity : 0.006 0.065 4329 Dihedral : 6.542 56.674 3498 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.59 % Favored : 96.09 % Rotamer: Outliers : 0.19 % Allowed : 4.78 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -1.30 (0.14), residues: 3122 helix: -0.08 (0.14), residues: 1242 sheet: 0.11 (0.19), residues: 591 loop : -2.11 (0.15), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 73 PHE 0.027 0.003 PHE 4 155 TYR 0.041 0.003 TYR 6 46 ARG 0.016 0.001 ARG 7 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1297 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.8653 (tp40) cc_final: 0.7700 (tm-30) REVERT: A 172 THR cc_start: 0.7294 (p) cc_final: 0.6492 (p) REVERT: A 182 ASP cc_start: 0.5736 (p0) cc_final: 0.5465 (p0) REVERT: A 208 ASN cc_start: 0.7859 (p0) cc_final: 0.7597 (p0) REVERT: A 211 VAL cc_start: 0.8203 (t) cc_final: 0.7015 (p) REVERT: A 242 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5956 (mm-30) REVERT: B 176 GLU cc_start: 0.6376 (mm-30) cc_final: 0.6115 (mm-30) REVERT: B 181 ASP cc_start: 0.7248 (m-30) cc_final: 0.6783 (m-30) REVERT: B 186 ASP cc_start: 0.6968 (p0) cc_final: 0.6737 (p0) REVERT: B 201 GLU cc_start: 0.5858 (tm-30) cc_final: 0.5282 (tm-30) REVERT: B 208 ASN cc_start: 0.6656 (p0) cc_final: 0.6281 (p0) REVERT: B 229 LEU cc_start: 0.7730 (mt) cc_final: 0.7329 (mt) REVERT: C 41 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8487 (tttt) REVERT: C 49 ILE cc_start: 0.7947 (tt) cc_final: 0.7690 (tt) REVERT: C 51 ASP cc_start: 0.8312 (t0) cc_final: 0.8025 (t0) REVERT: C 137 LEU cc_start: 0.8761 (mt) cc_final: 0.8310 (mt) REVERT: C 149 GLU cc_start: 0.8203 (tt0) cc_final: 0.7858 (tt0) REVERT: C 160 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7597 (mtmm) REVERT: C 164 ILE cc_start: 0.9304 (pt) cc_final: 0.9084 (pt) REVERT: C 199 SER cc_start: 0.8577 (p) cc_final: 0.7967 (t) REVERT: C 200 ILE cc_start: 0.8812 (pt) cc_final: 0.8225 (mt) REVERT: C 202 SER cc_start: 0.7892 (p) cc_final: 0.7327 (p) REVERT: C 208 ASN cc_start: 0.7376 (p0) cc_final: 0.6922 (p0) REVERT: C 209 ILE cc_start: 0.8444 (pt) cc_final: 0.8223 (pt) REVERT: C 214 VAL cc_start: 0.8520 (t) cc_final: 0.8164 (t) REVERT: C 217 ASP cc_start: 0.7282 (p0) cc_final: 0.6850 (p0) REVERT: D 64 ILE cc_start: 0.7181 (pt) cc_final: 0.6918 (pt) REVERT: D 95 GLU cc_start: 0.7310 (tt0) cc_final: 0.6065 (tt0) REVERT: D 115 LYS cc_start: 0.8492 (mttm) cc_final: 0.7950 (mtpt) REVERT: D 185 PHE cc_start: 0.6445 (t80) cc_final: 0.6018 (t80) REVERT: E 28 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: E 65 GLU cc_start: 0.5641 (tt0) cc_final: 0.4979 (tt0) REVERT: E 68 TYR cc_start: 0.8540 (m-80) cc_final: 0.8217 (m-80) REVERT: E 75 CYS cc_start: 0.8353 (p) cc_final: 0.8113 (p) REVERT: E 120 LYS cc_start: 0.8054 (mttt) cc_final: 0.7748 (mttm) REVERT: E 221 PHE cc_start: 0.8276 (t80) cc_final: 0.7954 (t80) REVERT: F 9 ASP cc_start: 0.8582 (p0) cc_final: 0.8145 (p0) REVERT: F 26 TYR cc_start: 0.8694 (m-10) cc_final: 0.8205 (m-10) REVERT: F 132 PHE cc_start: 0.8940 (m-80) cc_final: 0.8735 (m-10) REVERT: F 150 THR cc_start: 0.7625 (p) cc_final: 0.7258 (p) REVERT: F 196 MET cc_start: 0.7345 (tpp) cc_final: 0.6827 (tpp) REVERT: F 199 SER cc_start: 0.8314 (p) cc_final: 0.7786 (t) REVERT: F 203 GLU cc_start: 0.7959 (pm20) cc_final: 0.7619 (pt0) REVERT: F 210 GLU cc_start: 0.6528 (tt0) cc_final: 0.6147 (tt0) REVERT: F 237 ASN cc_start: 0.4761 (m-40) cc_final: 0.2631 (m-40) REVERT: G 23 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7755 (tp40) REVERT: G 33 ARG cc_start: 0.7545 (ptp-170) cc_final: 0.7280 (mtm180) REVERT: G 89 ILE cc_start: 0.9339 (mm) cc_final: 0.9009 (mm) REVERT: G 171 VAL cc_start: 0.7147 (t) cc_final: 0.5892 (p) REVERT: 1 72 ILE cc_start: 0.8913 (mm) cc_final: 0.8695 (mm) REVERT: 1 208 LEU cc_start: 0.3577 (pp) cc_final: 0.3360 (pp) REVERT: 2 19 CYS cc_start: 0.5344 (m) cc_final: 0.4983 (m) REVERT: 2 125 ILE cc_start: 0.8361 (mp) cc_final: 0.8142 (mp) REVERT: 2 172 ILE cc_start: 0.7125 (tp) cc_final: 0.6873 (tp) REVERT: 3 46 TYR cc_start: 0.7195 (m-80) cc_final: 0.6683 (m-10) REVERT: 4 48 ILE cc_start: 0.9121 (mm) cc_final: 0.8420 (mm) REVERT: 4 87 VAL cc_start: 0.8629 (t) cc_final: 0.8356 (t) REVERT: 4 88 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7294 (ttp-170) REVERT: 5 46 TYR cc_start: 0.7199 (m-80) cc_final: 0.6563 (m-80) REVERT: 5 79 ILE cc_start: 0.8575 (mt) cc_final: 0.8288 (mt) REVERT: 5 92 THR cc_start: 0.8503 (p) cc_final: 0.8288 (p) REVERT: 5 122 ILE cc_start: 0.7822 (mt) cc_final: 0.7440 (mt) REVERT: 5 146 THR cc_start: 0.6634 (p) cc_final: 0.6349 (p) REVERT: 6 81 ARG cc_start: 0.7578 (ttm110) cc_final: 0.7293 (tpp80) REVERT: 6 137 ILE cc_start: 0.7512 (mm) cc_final: 0.7292 (mp) outliers start: 5 outliers final: 0 residues processed: 1299 average time/residue: 0.3942 time to fit residues: 767.7868 Evaluate side-chains 1103 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1103 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 302 optimal weight: 0.0980 chunk 249 optimal weight: 0.7980 chunk 277 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 237 ASN 3 75 ASN 6 96 ASN 6 198 GLN 7 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24968 Z= 0.259 Angle : 0.739 14.150 33660 Z= 0.403 Chirality : 0.049 0.204 3881 Planarity : 0.005 0.083 4329 Dihedral : 5.947 59.367 3498 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer: Outliers : 0.27 % Allowed : 2.98 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3122 helix: 0.13 (0.14), residues: 1246 sheet: 0.24 (0.19), residues: 593 loop : -1.70 (0.15), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 73 PHE 0.025 0.002 PHE 5 155 TYR 0.029 0.002 TYR 6 148 ARG 0.012 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1237 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.8526 (tp40) cc_final: 0.7827 (tm-30) REVERT: A 182 ASP cc_start: 0.5810 (p0) cc_final: 0.5596 (p0) REVERT: A 186 ASP cc_start: 0.6929 (p0) cc_final: 0.6258 (p0) REVERT: A 211 VAL cc_start: 0.8467 (t) cc_final: 0.7280 (p) REVERT: B 38 ILE cc_start: 0.8427 (mt) cc_final: 0.7973 (mt) REVERT: B 151 ASP cc_start: 0.8347 (t0) cc_final: 0.8082 (t0) REVERT: B 152 PRO cc_start: 0.9638 (Cg_exo) cc_final: 0.9196 (Cg_endo) REVERT: B 181 ASP cc_start: 0.7148 (m-30) cc_final: 0.6934 (m-30) REVERT: B 187 ASP cc_start: 0.5918 (m-30) cc_final: 0.5349 (m-30) REVERT: B 201 GLU cc_start: 0.5579 (tm-30) cc_final: 0.5350 (tm-30) REVERT: B 208 ASN cc_start: 0.6535 (p0) cc_final: 0.6222 (p0) REVERT: B 238 GLU cc_start: 0.5334 (mt-10) cc_final: 0.4805 (mt-10) REVERT: C 9 ASP cc_start: 0.7595 (p0) cc_final: 0.7296 (p0) REVERT: C 49 ILE cc_start: 0.7914 (tt) cc_final: 0.7685 (tt) REVERT: C 123 TYR cc_start: 0.7701 (m-80) cc_final: 0.7295 (m-80) REVERT: C 202 SER cc_start: 0.7958 (p) cc_final: 0.7672 (p) REVERT: C 208 ASN cc_start: 0.7522 (p0) cc_final: 0.7063 (p0) REVERT: C 215 LYS cc_start: 0.6840 (mttt) cc_final: 0.6634 (mttp) REVERT: C 225 SER cc_start: 0.6896 (p) cc_final: 0.6401 (p) REVERT: D 18 ASP cc_start: 0.7755 (p0) cc_final: 0.7409 (p0) REVERT: D 57 LYS cc_start: 0.7675 (pttm) cc_final: 0.7372 (mppt) REVERT: D 64 ILE cc_start: 0.7043 (pt) cc_final: 0.6766 (pt) REVERT: D 115 LYS cc_start: 0.8428 (mttm) cc_final: 0.8130 (mtpt) REVERT: D 121 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7253 (tm-30) REVERT: D 174 PHE cc_start: 0.7119 (t80) cc_final: 0.6431 (t80) REVERT: D 178 GLU cc_start: 0.6319 (mt-10) cc_final: 0.6064 (mt-10) REVERT: D 240 ILE cc_start: 0.7581 (pt) cc_final: 0.7210 (pt) REVERT: E 68 TYR cc_start: 0.8384 (m-80) cc_final: 0.8044 (m-80) REVERT: E 186 ASP cc_start: 0.6366 (m-30) cc_final: 0.6121 (m-30) REVERT: E 200 ILE cc_start: 0.8533 (pt) cc_final: 0.8280 (pt) REVERT: E 218 ASP cc_start: 0.8126 (p0) cc_final: 0.7111 (p0) REVERT: F 9 ASP cc_start: 0.8569 (p0) cc_final: 0.8005 (p0) REVERT: F 22 PHE cc_start: 0.7982 (m-80) cc_final: 0.7643 (m-80) REVERT: F 26 TYR cc_start: 0.8648 (m-10) cc_final: 0.8223 (m-10) REVERT: F 120 LYS cc_start: 0.8433 (mtmm) cc_final: 0.7700 (ttmm) REVERT: F 132 PHE cc_start: 0.8845 (m-80) cc_final: 0.8636 (m-10) REVERT: F 150 THR cc_start: 0.7659 (p) cc_final: 0.7289 (p) REVERT: G 47 ILE cc_start: 0.8654 (mt) cc_final: 0.8295 (mt) REVERT: G 73 HIS cc_start: 0.6777 (p-80) cc_final: 0.6560 (p-80) REVERT: G 176 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5910 (mm-30) REVERT: G 211 VAL cc_start: 0.9079 (t) cc_final: 0.8806 (t) REVERT: 1 80 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8097 (mtt180) REVERT: 1 122 ILE cc_start: 0.7207 (mm) cc_final: 0.6946 (mm) REVERT: 1 173 TYR cc_start: 0.6061 (t80) cc_final: 0.5445 (t80) REVERT: 1 208 LEU cc_start: 0.3782 (pp) cc_final: 0.3574 (pp) REVERT: 2 19 CYS cc_start: 0.5315 (m) cc_final: 0.5031 (m) REVERT: 2 81 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8176 (mmt90) REVERT: 2 172 ILE cc_start: 0.7027 (tp) cc_final: 0.6782 (tp) REVERT: 2 203 GLU cc_start: 0.3687 (pt0) cc_final: 0.3254 (pt0) REVERT: 3 46 TYR cc_start: 0.7319 (m-80) cc_final: 0.6525 (m-80) REVERT: 3 48 ILE cc_start: 0.8909 (tp) cc_final: 0.8644 (tp) REVERT: 4 48 ILE cc_start: 0.9251 (mm) cc_final: 0.8788 (mm) REVERT: 4 80 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7589 (mtp180) REVERT: 4 83 ARG cc_start: 0.7610 (ptm160) cc_final: 0.7220 (ptm160) REVERT: 4 110 LEU cc_start: 0.8352 (mp) cc_final: 0.8078 (mp) REVERT: 4 123 TYR cc_start: 0.8584 (m-80) cc_final: 0.8210 (m-80) REVERT: 4 144 SER cc_start: 0.7182 (p) cc_final: 0.6900 (p) REVERT: 5 33 MET cc_start: 0.1765 (mtt) cc_final: 0.1000 (ttm) REVERT: 5 79 ILE cc_start: 0.8536 (mt) cc_final: 0.8020 (mt) REVERT: 5 92 THR cc_start: 0.8550 (p) cc_final: 0.8306 (p) REVERT: 5 165 VAL cc_start: 0.6604 (m) cc_final: 0.6275 (m) REVERT: 6 46 TYR cc_start: 0.7194 (m-10) cc_final: 0.6915 (m-10) REVERT: 6 72 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8403 (mp) REVERT: 6 79 ILE cc_start: 0.8902 (mt) cc_final: 0.8545 (mt) REVERT: 6 81 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7419 (tpp80) REVERT: 7 75 ASN cc_start: 0.7903 (m110) cc_final: 0.7695 (m-40) REVERT: 7 77 TYR cc_start: 0.7375 (t80) cc_final: 0.7150 (t80) REVERT: 7 79 ILE cc_start: 0.8842 (mt) cc_final: 0.8622 (mm) REVERT: 7 155 PHE cc_start: 0.7030 (t80) cc_final: 0.6759 (t80) REVERT: 7 193 GLU cc_start: 0.5155 (tm-30) cc_final: 0.4954 (tm-30) outliers start: 7 outliers final: 1 residues processed: 1241 average time/residue: 0.3810 time to fit residues: 718.5554 Evaluate side-chains 1109 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1107 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 145 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 297 optimal weight: 0.8980 chunk 146 optimal weight: 0.4980 chunk 266 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 5 GLN F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN 1 47 GLN 3 75 ASN 4 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 24968 Z= 0.269 Angle : 0.718 14.370 33660 Z= 0.388 Chirality : 0.048 0.206 3881 Planarity : 0.005 0.096 4329 Dihedral : 5.733 58.215 3498 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.78 % Favored : 95.90 % Rotamer: Outliers : 0.23 % Allowed : 3.48 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3122 helix: 0.25 (0.14), residues: 1228 sheet: 0.19 (0.19), residues: 618 loop : -1.57 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 73 PHE 0.022 0.002 PHE D 175 TYR 0.030 0.002 TYR 7 148 ARG 0.011 0.001 ARG 2 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1235 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.9322 (mt) cc_final: 0.8914 (mt) REVERT: A 166 MET cc_start: 0.6885 (mtp) cc_final: 0.6562 (ttt) REVERT: A 181 ASP cc_start: 0.5949 (m-30) cc_final: 0.5670 (m-30) REVERT: A 186 ASP cc_start: 0.6710 (p0) cc_final: 0.6068 (p0) REVERT: A 208 ASN cc_start: 0.7438 (p0) cc_final: 0.6976 (p0) REVERT: A 211 VAL cc_start: 0.8605 (t) cc_final: 0.7280 (p) REVERT: A 223 GLU cc_start: 0.6803 (tt0) cc_final: 0.6431 (tt0) REVERT: B 58 LEU cc_start: 0.8147 (mt) cc_final: 0.7860 (mt) REVERT: B 93 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7971 (mtt-85) REVERT: B 151 ASP cc_start: 0.8424 (t0) cc_final: 0.8182 (t0) REVERT: B 152 PRO cc_start: 0.9626 (Cg_exo) cc_final: 0.9187 (Cg_endo) REVERT: B 196 MET cc_start: 0.6851 (mmm) cc_final: 0.6610 (mmm) REVERT: B 201 GLU cc_start: 0.5896 (tm-30) cc_final: 0.5381 (tm-30) REVERT: B 208 ASN cc_start: 0.6731 (p0) cc_final: 0.6486 (p0) REVERT: B 238 GLU cc_start: 0.5028 (mt-10) cc_final: 0.4525 (mt-10) REVERT: C 31 VAL cc_start: 0.9121 (t) cc_final: 0.8858 (t) REVERT: C 123 TYR cc_start: 0.7630 (m-80) cc_final: 0.7312 (m-80) REVERT: C 202 SER cc_start: 0.8373 (p) cc_final: 0.8105 (p) REVERT: C 208 ASN cc_start: 0.7684 (p0) cc_final: 0.7242 (p0) REVERT: C 214 VAL cc_start: 0.8501 (t) cc_final: 0.8204 (t) REVERT: D 18 ASP cc_start: 0.7877 (p0) cc_final: 0.7571 (p0) REVERT: D 57 LYS cc_start: 0.7705 (pttm) cc_final: 0.7367 (mppt) REVERT: D 64 ILE cc_start: 0.7077 (pt) cc_final: 0.6751 (pt) REVERT: D 67 ILE cc_start: 0.8868 (mm) cc_final: 0.8654 (mm) REVERT: D 68 TYR cc_start: 0.6681 (m-80) cc_final: 0.6463 (m-80) REVERT: D 91 ARG cc_start: 0.8301 (tpt90) cc_final: 0.8041 (tpt170) REVERT: D 108 THR cc_start: 0.9059 (p) cc_final: 0.8845 (m) REVERT: D 121 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7221 (tm-30) REVERT: D 200 ILE cc_start: 0.8124 (pt) cc_final: 0.7904 (pt) REVERT: D 240 ILE cc_start: 0.7636 (pt) cc_final: 0.7105 (pt) REVERT: E 8 TYR cc_start: 0.7576 (m-10) cc_final: 0.6765 (m-80) REVERT: E 21 LEU cc_start: 0.7433 (mt) cc_final: 0.7164 (mp) REVERT: E 52 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7697 (ttpp) REVERT: E 218 ASP cc_start: 0.7906 (p0) cc_final: 0.6916 (p0) REVERT: F 9 ASP cc_start: 0.8477 (p0) cc_final: 0.7718 (p0) REVERT: F 22 PHE cc_start: 0.7891 (m-80) cc_final: 0.7673 (m-80) REVERT: F 26 TYR cc_start: 0.8648 (m-10) cc_final: 0.8204 (m-10) REVERT: F 84 ASP cc_start: 0.7329 (m-30) cc_final: 0.7119 (m-30) REVERT: F 99 ASN cc_start: 0.8223 (t0) cc_final: 0.7868 (t0) REVERT: F 120 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8034 (mtmm) REVERT: F 150 THR cc_start: 0.7849 (p) cc_final: 0.7501 (p) REVERT: F 228 GLU cc_start: 0.6490 (tp30) cc_final: 0.6239 (tp30) REVERT: F 232 TYR cc_start: 0.6926 (m-80) cc_final: 0.6475 (m-10) REVERT: G 16 SER cc_start: 0.7993 (p) cc_final: 0.7632 (t) REVERT: G 73 HIS cc_start: 0.7272 (p-80) cc_final: 0.6734 (p-80) REVERT: G 143 GLU cc_start: 0.6324 (pm20) cc_final: 0.5774 (pm20) REVERT: G 211 VAL cc_start: 0.9137 (t) cc_final: 0.8491 (t) REVERT: 1 80 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7974 (mtt180) REVERT: 1 86 THR cc_start: 0.8552 (t) cc_final: 0.7742 (t) REVERT: 1 123 TYR cc_start: 0.8011 (m-80) cc_final: 0.7648 (m-80) REVERT: 1 173 TYR cc_start: 0.5887 (t80) cc_final: 0.5229 (t80) REVERT: 1 190 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7869 (ptmt) REVERT: 2 48 ILE cc_start: 0.8428 (mm) cc_final: 0.8190 (mm) REVERT: 2 52 MET cc_start: 0.6230 (ttm) cc_final: 0.5866 (ttm) REVERT: 2 116 ASP cc_start: 0.4667 (p0) cc_final: 0.3501 (p0) REVERT: 2 197 TYR cc_start: 0.4816 (t80) cc_final: 0.4433 (t80) REVERT: 3 46 TYR cc_start: 0.7369 (m-80) cc_final: 0.6879 (m-80) REVERT: 3 87 VAL cc_start: 0.8297 (t) cc_final: 0.8070 (t) REVERT: 3 121 SER cc_start: 0.7269 (p) cc_final: 0.7056 (p) REVERT: 3 138 VAL cc_start: 0.7396 (p) cc_final: 0.7088 (p) REVERT: 4 48 ILE cc_start: 0.9223 (mm) cc_final: 0.8821 (mm) REVERT: 4 80 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7570 (mtp180) REVERT: 4 123 TYR cc_start: 0.8486 (m-80) cc_final: 0.7831 (m-80) REVERT: 5 33 MET cc_start: 0.1750 (mtt) cc_final: 0.0764 (ttm) REVERT: 5 46 TYR cc_start: 0.7721 (m-80) cc_final: 0.7080 (m-10) REVERT: 5 165 VAL cc_start: 0.6297 (m) cc_final: 0.5991 (m) REVERT: 6 68 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7405 (ttp-110) REVERT: 6 79 ILE cc_start: 0.8705 (mt) cc_final: 0.8265 (mt) REVERT: 7 84 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8382 (mmtt) REVERT: 7 193 GLU cc_start: 0.5332 (tm-30) cc_final: 0.5056 (tm-30) outliers start: 6 outliers final: 0 residues processed: 1237 average time/residue: 0.3600 time to fit residues: 685.4008 Evaluate side-chains 1116 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1116 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 267 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN 1 47 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 99 ASN ** 3 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 75 ASN ** 7 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24968 Z= 0.278 Angle : 0.727 14.410 33660 Z= 0.391 Chirality : 0.048 0.237 3881 Planarity : 0.004 0.046 4329 Dihedral : 5.678 62.525 3498 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.10 % Favored : 95.64 % Rotamer: Outliers : 0.19 % Allowed : 2.29 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3122 helix: 0.25 (0.15), residues: 1225 sheet: 0.21 (0.19), residues: 613 loop : -1.51 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 73 PHE 0.028 0.002 PHE C 175 TYR 0.030 0.002 TYR 7 148 ARG 0.007 0.001 ARG 5 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1241 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9155 (m) cc_final: 0.8745 (p) REVERT: A 166 MET cc_start: 0.7022 (mtp) cc_final: 0.6629 (ttt) REVERT: A 186 ASP cc_start: 0.6645 (p0) cc_final: 0.6048 (p0) REVERT: A 208 ASN cc_start: 0.7654 (p0) cc_final: 0.7171 (p0) REVERT: A 211 VAL cc_start: 0.8693 (t) cc_final: 0.7524 (p) REVERT: B 20 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7507 (ptp-170) REVERT: B 78 THR cc_start: 0.8687 (t) cc_final: 0.8465 (m) REVERT: B 174 PHE cc_start: 0.7440 (t80) cc_final: 0.6965 (t80) REVERT: B 186 ASP cc_start: 0.6649 (p0) cc_final: 0.6405 (p0) REVERT: B 201 GLU cc_start: 0.5848 (tm-30) cc_final: 0.5296 (tm-30) REVERT: B 208 ASN cc_start: 0.6853 (p0) cc_final: 0.6631 (p0) REVERT: B 238 GLU cc_start: 0.5098 (mt-10) cc_final: 0.4805 (mt-10) REVERT: C 52 LYS cc_start: 0.7908 (mtpp) cc_final: 0.6964 (mtpp) REVERT: C 120 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8425 (mtmm) REVERT: C 123 TYR cc_start: 0.7567 (m-80) cc_final: 0.7210 (m-80) REVERT: C 202 SER cc_start: 0.8430 (p) cc_final: 0.8149 (p) REVERT: C 214 VAL cc_start: 0.8570 (t) cc_final: 0.8266 (t) REVERT: D 108 THR cc_start: 0.8969 (p) cc_final: 0.8756 (m) REVERT: D 121 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 186 ASP cc_start: 0.7700 (p0) cc_final: 0.7466 (p0) REVERT: D 240 ILE cc_start: 0.7566 (pt) cc_final: 0.7272 (pt) REVERT: E 8 TYR cc_start: 0.7681 (m-10) cc_final: 0.6915 (m-80) REVERT: E 25 GLU cc_start: 0.6438 (tp30) cc_final: 0.5569 (tp30) REVERT: E 28 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7631 (mmm160) REVERT: E 44 GLU cc_start: 0.5492 (pm20) cc_final: 0.5116 (pt0) REVERT: E 108 THR cc_start: 0.8224 (m) cc_final: 0.7964 (m) REVERT: E 210 GLU cc_start: 0.5688 (mm-30) cc_final: 0.5153 (mm-30) REVERT: E 218 ASP cc_start: 0.7881 (p0) cc_final: 0.7233 (p0) REVERT: F 9 ASP cc_start: 0.8531 (p0) cc_final: 0.7813 (p0) REVERT: F 22 PHE cc_start: 0.8216 (m-80) cc_final: 0.8004 (m-10) REVERT: F 26 TYR cc_start: 0.8643 (m-10) cc_final: 0.8240 (m-10) REVERT: F 52 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8580 (mtpp) REVERT: F 150 THR cc_start: 0.7904 (p) cc_final: 0.7650 (p) REVERT: F 229 LEU cc_start: 0.7501 (tt) cc_final: 0.7254 (tt) REVERT: F 232 TYR cc_start: 0.7066 (m-80) cc_final: 0.6847 (m-10) REVERT: G 16 SER cc_start: 0.8265 (p) cc_final: 0.7863 (t) REVERT: G 47 ILE cc_start: 0.8594 (mt) cc_final: 0.8356 (mt) REVERT: G 66 LYS cc_start: 0.8187 (tptt) cc_final: 0.7850 (mppt) REVERT: G 72 GLU cc_start: 0.5066 (mp0) cc_final: 0.4706 (mp0) REVERT: G 172 THR cc_start: 0.6864 (p) cc_final: 0.5699 (p) REVERT: G 191 LEU cc_start: 0.7906 (tp) cc_final: 0.7389 (tp) REVERT: G 211 VAL cc_start: 0.8987 (t) cc_final: 0.8680 (p) REVERT: 1 86 THR cc_start: 0.8155 (t) cc_final: 0.7941 (t) REVERT: 1 122 ILE cc_start: 0.7734 (mm) cc_final: 0.7500 (mm) REVERT: 1 123 TYR cc_start: 0.7989 (m-80) cc_final: 0.7558 (m-80) REVERT: 1 173 TYR cc_start: 0.6025 (t80) cc_final: 0.5412 (t80) REVERT: 1 190 LYS cc_start: 0.8033 (ptpp) cc_final: 0.7827 (ptmm) REVERT: 1 193 GLU cc_start: 0.6325 (tm-30) cc_final: 0.5862 (tm-30) REVERT: 2 48 ILE cc_start: 0.8503 (mm) cc_final: 0.8250 (mm) REVERT: 2 52 MET cc_start: 0.6305 (ttm) cc_final: 0.5834 (ttt) REVERT: 2 83 ARG cc_start: 0.7225 (ptm160) cc_final: 0.6762 (ptt180) REVERT: 2 197 TYR cc_start: 0.4793 (t80) cc_final: 0.4529 (t80) REVERT: 2 203 GLU cc_start: 0.3668 (pt0) cc_final: 0.3237 (pt0) REVERT: 3 44 LYS cc_start: 0.7192 (tptt) cc_final: 0.6844 (mptt) REVERT: 3 46 TYR cc_start: 0.7379 (m-80) cc_final: 0.6814 (m-80) REVERT: 3 86 THR cc_start: 0.7809 (p) cc_final: 0.7497 (p) REVERT: 3 87 VAL cc_start: 0.8353 (t) cc_final: 0.8040 (t) REVERT: 3 121 SER cc_start: 0.7501 (p) cc_final: 0.7210 (p) REVERT: 4 48 ILE cc_start: 0.9222 (mm) cc_final: 0.8686 (mm) REVERT: 4 80 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7673 (mtp180) REVERT: 5 46 TYR cc_start: 0.7925 (m-80) cc_final: 0.7694 (m-10) REVERT: 6 25 MET cc_start: 0.4604 (mtp) cc_final: 0.4297 (mtp) REVERT: 6 68 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7649 (ttp-110) REVERT: 7 193 GLU cc_start: 0.5347 (tm-30) cc_final: 0.5113 (tm-30) outliers start: 5 outliers final: 0 residues processed: 1244 average time/residue: 0.3807 time to fit residues: 721.5461 Evaluate side-chains 1110 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1110 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 0.1980 chunk 247 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 198 GLN 4 75 ASN ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24968 Z= 0.296 Angle : 0.738 14.428 33660 Z= 0.394 Chirality : 0.048 0.204 3881 Planarity : 0.004 0.048 4329 Dihedral : 5.644 58.988 3498 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3122 helix: 0.25 (0.15), residues: 1220 sheet: 0.18 (0.19), residues: 616 loop : -1.40 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 73 PHE 0.023 0.002 PHE 6 196 TYR 0.032 0.002 TYR 7 148 ARG 0.009 0.001 ARG 1 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1224 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9179 (m) cc_final: 0.8804 (p) REVERT: A 69 LYS cc_start: 0.8814 (tttm) cc_final: 0.8470 (tttm) REVERT: A 166 MET cc_start: 0.6942 (mtp) cc_final: 0.6412 (ttt) REVERT: A 181 ASP cc_start: 0.5852 (m-30) cc_final: 0.5602 (m-30) REVERT: A 186 ASP cc_start: 0.6608 (p0) cc_final: 0.6067 (p0) REVERT: A 196 MET cc_start: 0.7919 (mmm) cc_final: 0.7704 (tpp) REVERT: A 208 ASN cc_start: 0.7451 (p0) cc_final: 0.7099 (p0) REVERT: A 211 VAL cc_start: 0.8389 (t) cc_final: 0.7579 (p) REVERT: A 229 LEU cc_start: 0.7784 (mt) cc_final: 0.7544 (mt) REVERT: B 38 ILE cc_start: 0.8478 (mt) cc_final: 0.8235 (mt) REVERT: B 130 ARG cc_start: 0.8620 (pmt-80) cc_final: 0.8373 (ppt170) REVERT: B 174 PHE cc_start: 0.7423 (t80) cc_final: 0.7053 (t80) REVERT: B 196 MET cc_start: 0.7380 (mmt) cc_final: 0.7068 (mmt) REVERT: B 201 GLU cc_start: 0.5938 (tm-30) cc_final: 0.5310 (tm-30) REVERT: B 208 ASN cc_start: 0.6909 (p0) cc_final: 0.6680 (p0) REVERT: B 229 LEU cc_start: 0.7791 (mt) cc_final: 0.7547 (mt) REVERT: B 238 GLU cc_start: 0.5178 (mt-10) cc_final: 0.4758 (mt-10) REVERT: C 12 ILE cc_start: 0.8859 (tp) cc_final: 0.8622 (tp) REVERT: C 52 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7165 (mtpp) REVERT: C 110 LYS cc_start: 0.8507 (tptp) cc_final: 0.8183 (tptt) REVERT: C 196 MET cc_start: 0.7167 (tpp) cc_final: 0.6895 (tpp) REVERT: C 202 SER cc_start: 0.8509 (p) cc_final: 0.8224 (p) REVERT: C 214 VAL cc_start: 0.8541 (t) cc_final: 0.8328 (t) REVERT: C 216 VAL cc_start: 0.8492 (m) cc_final: 0.8244 (m) REVERT: C 217 ASP cc_start: 0.7482 (p0) cc_final: 0.7096 (p0) REVERT: D 108 THR cc_start: 0.9035 (p) cc_final: 0.8753 (m) REVERT: D 121 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 185 PHE cc_start: 0.7016 (t80) cc_final: 0.6445 (t80) REVERT: D 240 ILE cc_start: 0.7428 (pt) cc_final: 0.7198 (pt) REVERT: E 8 TYR cc_start: 0.7801 (m-10) cc_final: 0.7048 (m-80) REVERT: E 25 GLU cc_start: 0.6417 (tp30) cc_final: 0.5784 (tp30) REVERT: E 28 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7416 (mmm160) REVERT: E 52 LYS cc_start: 0.7603 (ttpp) cc_final: 0.7165 (ttpp) REVERT: E 120 LYS cc_start: 0.8238 (mttm) cc_final: 0.8005 (mttm) REVERT: E 148 TYR cc_start: 0.9191 (m-80) cc_final: 0.8655 (m-10) REVERT: E 186 ASP cc_start: 0.6253 (m-30) cc_final: 0.5294 (m-30) REVERT: E 218 ASP cc_start: 0.7646 (p0) cc_final: 0.7220 (p0) REVERT: F 9 ASP cc_start: 0.8594 (p0) cc_final: 0.7942 (p0) REVERT: F 26 TYR cc_start: 0.8750 (m-10) cc_final: 0.8326 (m-10) REVERT: F 52 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8668 (mtpp) REVERT: F 194 VAL cc_start: 0.8086 (t) cc_final: 0.7869 (t) REVERT: F 232 TYR cc_start: 0.6901 (m-80) cc_final: 0.6662 (m-10) REVERT: G 16 SER cc_start: 0.8389 (p) cc_final: 0.8156 (p) REVERT: G 73 HIS cc_start: 0.7231 (p-80) cc_final: 0.6532 (p90) REVERT: G 181 ASP cc_start: 0.6585 (p0) cc_final: 0.6373 (p0) REVERT: G 211 VAL cc_start: 0.9083 (t) cc_final: 0.8816 (t) REVERT: G 234 GLU cc_start: 0.6547 (pp20) cc_final: 0.5699 (pp20) REVERT: 1 173 TYR cc_start: 0.5948 (t80) cc_final: 0.5372 (t80) REVERT: 1 190 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7759 (ptmm) REVERT: 2 48 ILE cc_start: 0.8466 (mm) cc_final: 0.8094 (mm) REVERT: 2 52 MET cc_start: 0.6162 (ttm) cc_final: 0.5663 (ttm) REVERT: 2 83 ARG cc_start: 0.7279 (ptm160) cc_final: 0.6926 (ptt180) REVERT: 3 46 TYR cc_start: 0.7245 (m-80) cc_final: 0.6960 (m-80) REVERT: 3 86 THR cc_start: 0.7834 (p) cc_final: 0.7520 (p) REVERT: 3 121 SER cc_start: 0.7394 (p) cc_final: 0.7032 (p) REVERT: 4 48 ILE cc_start: 0.9241 (mm) cc_final: 0.8889 (mm) REVERT: 4 80 ARG cc_start: 0.8411 (mtp180) cc_final: 0.7745 (mtp180) REVERT: 4 84 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7797 (mtpt) REVERT: 4 151 LEU cc_start: 0.6452 (tp) cc_final: 0.6197 (tp) REVERT: 5 46 TYR cc_start: 0.7538 (m-80) cc_final: 0.7125 (m-10) REVERT: 6 68 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7888 (ttp-110) REVERT: 7 93 LEU cc_start: 0.8966 (tp) cc_final: 0.8711 (tp) REVERT: 7 134 GLU cc_start: 0.7524 (mp0) cc_final: 0.6256 (mp0) REVERT: 7 193 GLU cc_start: 0.5071 (tm-30) cc_final: 0.4712 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1224 average time/residue: 0.3662 time to fit residues: 697.4142 Evaluate side-chains 1113 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1113 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.0050 chunk 33 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 250 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 137 optimal weight: 0.0980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24968 Z= 0.248 Angle : 0.729 14.024 33660 Z= 0.390 Chirality : 0.049 0.270 3881 Planarity : 0.004 0.050 4329 Dihedral : 5.640 57.944 3498 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.75 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3122 helix: 0.26 (0.15), residues: 1217 sheet: 0.11 (0.19), residues: 624 loop : -1.38 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.032 0.002 PHE B 175 TYR 0.032 0.002 TYR 7 148 ARG 0.009 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1196 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7359 (tt0) cc_final: 0.6577 (tt0) REVERT: A 31 VAL cc_start: 0.9171 (m) cc_final: 0.8645 (p) REVERT: A 69 LYS cc_start: 0.8590 (tttm) cc_final: 0.8299 (tttm) REVERT: A 121 GLN cc_start: 0.7992 (tp40) cc_final: 0.7695 (tp40) REVERT: A 166 MET cc_start: 0.6850 (mtp) cc_final: 0.6382 (ttt) REVERT: A 208 ASN cc_start: 0.7420 (p0) cc_final: 0.6910 (p0) REVERT: A 211 VAL cc_start: 0.8464 (t) cc_final: 0.7716 (p) REVERT: B 78 THR cc_start: 0.8765 (t) cc_final: 0.8558 (m) REVERT: B 130 ARG cc_start: 0.8625 (pmt-80) cc_final: 0.8380 (ppt170) REVERT: B 174 PHE cc_start: 0.7636 (t80) cc_final: 0.7289 (t80) REVERT: B 177 LYS cc_start: 0.7901 (tptt) cc_final: 0.7637 (tptt) REVERT: B 181 ASP cc_start: 0.6837 (m-30) cc_final: 0.6552 (m-30) REVERT: B 186 ASP cc_start: 0.6807 (p0) cc_final: 0.6506 (p0) REVERT: B 196 MET cc_start: 0.7339 (mmt) cc_final: 0.6631 (mmm) REVERT: B 198 LEU cc_start: 0.7585 (mt) cc_final: 0.7261 (mt) REVERT: B 201 GLU cc_start: 0.5832 (tm-30) cc_final: 0.5627 (tm-30) REVERT: B 208 ASN cc_start: 0.6840 (p0) cc_final: 0.6597 (p0) REVERT: B 229 LEU cc_start: 0.7954 (mt) cc_final: 0.7700 (mt) REVERT: C 14 VAL cc_start: 0.8584 (t) cc_final: 0.8316 (t) REVERT: C 52 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7259 (mtpp) REVERT: C 91 ARG cc_start: 0.7814 (mmm160) cc_final: 0.6737 (tpt170) REVERT: C 110 LYS cc_start: 0.8343 (tptp) cc_final: 0.8088 (tptt) REVERT: C 148 TYR cc_start: 0.8968 (m-80) cc_final: 0.8742 (m-10) REVERT: C 202 SER cc_start: 0.8508 (p) cc_final: 0.8199 (p) REVERT: C 214 VAL cc_start: 0.8361 (t) cc_final: 0.7971 (t) REVERT: C 216 VAL cc_start: 0.8207 (m) cc_final: 0.7703 (m) REVERT: C 217 ASP cc_start: 0.7115 (p0) cc_final: 0.6705 (p0) REVERT: D 64 ILE cc_start: 0.7225 (pt) cc_final: 0.6999 (pt) REVERT: D 121 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7339 (tm-30) REVERT: D 130 ARG cc_start: 0.8108 (ptt-90) cc_final: 0.7648 (ptt-90) REVERT: D 240 ILE cc_start: 0.7422 (pt) cc_final: 0.7065 (pt) REVERT: E 8 TYR cc_start: 0.7734 (m-10) cc_final: 0.6905 (m-80) REVERT: E 25 GLU cc_start: 0.6420 (tp30) cc_final: 0.5783 (tp30) REVERT: E 168 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7824 (tpt-90) REVERT: E 183 LEU cc_start: 0.5696 (pt) cc_final: 0.5081 (pt) REVERT: E 186 ASP cc_start: 0.6387 (m-30) cc_final: 0.5394 (m-30) REVERT: E 218 ASP cc_start: 0.7673 (p0) cc_final: 0.7217 (p0) REVERT: F 9 ASP cc_start: 0.8647 (p0) cc_final: 0.7909 (p0) REVERT: F 26 TYR cc_start: 0.8589 (m-10) cc_final: 0.8272 (m-10) REVERT: F 52 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8609 (mtpp) REVERT: F 185 PHE cc_start: 0.7006 (t80) cc_final: 0.6689 (t80) REVERT: F 200 ILE cc_start: 0.8776 (mm) cc_final: 0.8339 (mm) REVERT: F 232 TYR cc_start: 0.7169 (m-80) cc_final: 0.6950 (m-10) REVERT: G 36 THR cc_start: 0.8719 (p) cc_final: 0.8514 (p) REVERT: G 41 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7938 (ttpt) REVERT: G 52 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8109 (pttp) REVERT: G 73 HIS cc_start: 0.7188 (p-80) cc_final: 0.6860 (p90) REVERT: G 172 THR cc_start: 0.6981 (p) cc_final: 0.6351 (p) REVERT: G 181 ASP cc_start: 0.6488 (p0) cc_final: 0.6052 (p0) REVERT: G 191 LEU cc_start: 0.7535 (tp) cc_final: 0.7288 (tp) REVERT: G 211 VAL cc_start: 0.9123 (t) cc_final: 0.8904 (t) REVERT: G 234 GLU cc_start: 0.6378 (pp20) cc_final: 0.5594 (pp20) REVERT: 1 17 LEU cc_start: 0.7804 (pt) cc_final: 0.7406 (pt) REVERT: 1 123 TYR cc_start: 0.7990 (m-80) cc_final: 0.7643 (m-80) REVERT: 1 172 ILE cc_start: 0.6169 (mm) cc_final: 0.5432 (mm) REVERT: 1 173 TYR cc_start: 0.6060 (t80) cc_final: 0.5439 (t80) REVERT: 2 45 ILE cc_start: 0.7694 (tt) cc_final: 0.7270 (tt) REVERT: 2 48 ILE cc_start: 0.8508 (mm) cc_final: 0.8179 (mm) REVERT: 2 52 MET cc_start: 0.5971 (ttm) cc_final: 0.5604 (ttt) REVERT: 2 83 ARG cc_start: 0.7165 (ptm160) cc_final: 0.6771 (ptt180) REVERT: 3 46 TYR cc_start: 0.7320 (m-80) cc_final: 0.6790 (m-80) REVERT: 3 48 ILE cc_start: 0.8651 (tp) cc_final: 0.8386 (tp) REVERT: 3 83 ARG cc_start: 0.5851 (ptp-170) cc_final: 0.5586 (ptp-170) REVERT: 3 87 VAL cc_start: 0.8394 (t) cc_final: 0.8152 (t) REVERT: 3 121 SER cc_start: 0.7538 (p) cc_final: 0.7057 (p) REVERT: 4 48 ILE cc_start: 0.9251 (mm) cc_final: 0.8878 (mm) REVERT: 4 80 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7763 (mtp180) REVERT: 4 87 VAL cc_start: 0.8408 (t) cc_final: 0.8150 (t) REVERT: 4 123 TYR cc_start: 0.8475 (m-80) cc_final: 0.6307 (m-80) REVERT: 4 191 ILE cc_start: 0.7946 (tp) cc_final: 0.7730 (tp) REVERT: 5 46 TYR cc_start: 0.7549 (m-80) cc_final: 0.7178 (m-10) REVERT: 5 146 THR cc_start: 0.6909 (p) cc_final: 0.6660 (p) REVERT: 7 93 LEU cc_start: 0.8988 (tp) cc_final: 0.8772 (tp) REVERT: 7 193 GLU cc_start: 0.4989 (tm-30) cc_final: 0.4632 (tm-30) REVERT: H 396 MET cc_start: 0.6935 (mpp) cc_final: 0.6151 (mpp) outliers start: 0 outliers final: 0 residues processed: 1196 average time/residue: 0.3714 time to fit residues: 687.2398 Evaluate side-chains 1103 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1103 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 96 ASN ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24968 Z= 0.267 Angle : 0.744 13.987 33660 Z= 0.395 Chirality : 0.049 0.273 3881 Planarity : 0.004 0.061 4329 Dihedral : 5.617 60.488 3498 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3122 helix: 0.20 (0.14), residues: 1246 sheet: 0.11 (0.19), residues: 621 loop : -1.36 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 73 PHE 0.019 0.002 PHE 7 65 TYR 0.033 0.002 TYR 7 148 ARG 0.011 0.001 ARG 1 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1187 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7643 (ptt-90) REVERT: A 166 MET cc_start: 0.7067 (mtp) cc_final: 0.6691 (ttt) REVERT: A 182 ASP cc_start: 0.6422 (p0) cc_final: 0.6130 (p0) REVERT: A 208 ASN cc_start: 0.7671 (p0) cc_final: 0.7430 (p0) REVERT: A 211 VAL cc_start: 0.8216 (t) cc_final: 0.7659 (p) REVERT: B 130 ARG cc_start: 0.8655 (pmt-80) cc_final: 0.8394 (ppt170) REVERT: B 181 ASP cc_start: 0.6905 (m-30) cc_final: 0.6700 (m-30) REVERT: B 186 ASP cc_start: 0.6684 (p0) cc_final: 0.6334 (p0) REVERT: C 14 VAL cc_start: 0.8532 (t) cc_final: 0.8234 (t) REVERT: C 52 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7253 (mtpp) REVERT: C 91 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7269 (tpt170) REVERT: C 110 LYS cc_start: 0.8410 (tptp) cc_final: 0.8164 (tptt) REVERT: C 182 ASP cc_start: 0.5818 (p0) cc_final: 0.5125 (p0) REVERT: C 196 MET cc_start: 0.6995 (tpp) cc_final: 0.6651 (tpp) REVERT: C 202 SER cc_start: 0.8506 (p) cc_final: 0.8232 (p) REVERT: C 214 VAL cc_start: 0.8357 (t) cc_final: 0.8003 (t) REVERT: C 217 ASP cc_start: 0.6989 (p0) cc_final: 0.6667 (p0) REVERT: D 67 ILE cc_start: 0.9000 (mm) cc_final: 0.8792 (mm) REVERT: D 104 ASP cc_start: 0.7453 (t0) cc_final: 0.7181 (t0) REVERT: D 121 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7320 (tm-30) REVERT: D 130 ARG cc_start: 0.8214 (ptt-90) cc_final: 0.7808 (ptt-90) REVERT: D 186 ASP cc_start: 0.7478 (p0) cc_final: 0.7249 (p0) REVERT: D 200 ILE cc_start: 0.8114 (pt) cc_final: 0.7552 (mm) REVERT: E 8 TYR cc_start: 0.7788 (m-10) cc_final: 0.6853 (m-80) REVERT: E 25 GLU cc_start: 0.6418 (tp30) cc_final: 0.5778 (tp30) REVERT: E 28 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7250 (mmm160) REVERT: E 53 ARG cc_start: 0.7804 (ptp-110) cc_final: 0.7568 (ptp-110) REVERT: E 186 ASP cc_start: 0.6107 (m-30) cc_final: 0.5068 (m-30) REVERT: F 9 ASP cc_start: 0.8443 (p0) cc_final: 0.7614 (p0) REVERT: F 26 TYR cc_start: 0.8620 (m-10) cc_final: 0.8365 (m-10) REVERT: F 52 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8579 (mtpt) REVERT: F 107 ILE cc_start: 0.9182 (tt) cc_final: 0.8950 (tt) REVERT: F 172 THR cc_start: 0.8332 (p) cc_final: 0.8130 (p) REVERT: F 196 MET cc_start: 0.7255 (tpp) cc_final: 0.6708 (tpp) REVERT: F 199 SER cc_start: 0.8566 (p) cc_final: 0.8257 (p) REVERT: F 200 ILE cc_start: 0.8982 (mm) cc_final: 0.8718 (mm) REVERT: G 41 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7694 (ttpt) REVERT: G 47 ILE cc_start: 0.8377 (mt) cc_final: 0.7588 (mt) REVERT: G 73 HIS cc_start: 0.7169 (p-80) cc_final: 0.6772 (p90) REVERT: G 143 GLU cc_start: 0.6859 (pm20) cc_final: 0.6313 (pm20) REVERT: G 174 PHE cc_start: 0.7310 (t80) cc_final: 0.6975 (t80) REVERT: G 181 ASP cc_start: 0.6051 (p0) cc_final: 0.5840 (p0) REVERT: G 191 LEU cc_start: 0.7552 (tp) cc_final: 0.7238 (tp) REVERT: G 211 VAL cc_start: 0.9156 (t) cc_final: 0.8684 (p) REVERT: G 234 GLU cc_start: 0.6298 (pp20) cc_final: 0.5644 (pp20) REVERT: 1 17 LEU cc_start: 0.7804 (pt) cc_final: 0.7502 (pt) REVERT: 1 87 VAL cc_start: 0.8792 (t) cc_final: 0.8584 (p) REVERT: 1 123 TYR cc_start: 0.7806 (m-80) cc_final: 0.7522 (m-80) REVERT: 1 172 ILE cc_start: 0.6200 (mm) cc_final: 0.5553 (mm) REVERT: 1 173 TYR cc_start: 0.6108 (t80) cc_final: 0.5480 (t80) REVERT: 2 45 ILE cc_start: 0.7554 (tt) cc_final: 0.7137 (tt) REVERT: 2 48 ILE cc_start: 0.8687 (mm) cc_final: 0.8411 (mm) REVERT: 2 83 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6768 (ptt180) REVERT: 3 46 TYR cc_start: 0.7360 (m-80) cc_final: 0.6746 (m-80) REVERT: 3 54 MET cc_start: 0.6961 (ttp) cc_final: 0.6732 (ttm) REVERT: 3 87 VAL cc_start: 0.8364 (t) cc_final: 0.7867 (t) REVERT: 3 94 THR cc_start: 0.8291 (p) cc_final: 0.8086 (p) REVERT: 3 121 SER cc_start: 0.7639 (p) cc_final: 0.7254 (p) REVERT: 3 138 VAL cc_start: 0.7493 (p) cc_final: 0.7214 (p) REVERT: 4 48 ILE cc_start: 0.9256 (mm) cc_final: 0.8828 (mm) REVERT: 4 68 ARG cc_start: 0.8415 (tpp80) cc_final: 0.8123 (tpp80) REVERT: 4 87 VAL cc_start: 0.8434 (t) cc_final: 0.8147 (t) REVERT: 4 120 LYS cc_start: 0.7584 (mtmt) cc_final: 0.7380 (mtpt) REVERT: 4 123 TYR cc_start: 0.8738 (m-80) cc_final: 0.7037 (m-80) REVERT: 4 137 ILE cc_start: 0.8543 (mm) cc_final: 0.8056 (mm) REVERT: 4 191 ILE cc_start: 0.7773 (tp) cc_final: 0.7466 (tp) REVERT: 5 46 TYR cc_start: 0.7462 (m-80) cc_final: 0.7222 (m-10) REVERT: 5 92 THR cc_start: 0.8202 (p) cc_final: 0.7779 (p) REVERT: 5 146 THR cc_start: 0.6990 (p) cc_final: 0.6751 (p) REVERT: 5 191 ILE cc_start: 0.7191 (mt) cc_final: 0.6928 (mt) REVERT: 6 64 GLN cc_start: 0.6826 (pp30) cc_final: 0.6387 (pp30) REVERT: 6 65 PHE cc_start: 0.8053 (t80) cc_final: 0.7789 (t80) REVERT: 7 77 TYR cc_start: 0.7691 (t80) cc_final: 0.6953 (t80) REVERT: 7 81 ARG cc_start: 0.6209 (mtp180) cc_final: 0.5863 (mtp180) REVERT: 7 193 GLU cc_start: 0.5195 (tm-30) cc_final: 0.4813 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1187 average time/residue: 0.3683 time to fit residues: 677.6315 Evaluate side-chains 1088 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1088 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 166 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 249 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 275 optimal weight: 0.0870 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24968 Z= 0.261 Angle : 0.761 13.775 33660 Z= 0.403 Chirality : 0.049 0.293 3881 Planarity : 0.005 0.095 4329 Dihedral : 5.600 61.765 3498 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3122 helix: 0.26 (0.15), residues: 1200 sheet: 0.07 (0.19), residues: 622 loop : -1.33 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 73 PHE 0.027 0.002 PHE C 185 TYR 0.046 0.002 TYR 6 46 ARG 0.011 0.001 ARG 1 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1189 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.7992 (ptt90) cc_final: 0.7373 (ptt-90) REVERT: A 166 MET cc_start: 0.7066 (mtp) cc_final: 0.6835 (ttp) REVERT: A 208 ASN cc_start: 0.7725 (p0) cc_final: 0.7226 (p0) REVERT: A 211 VAL cc_start: 0.8263 (t) cc_final: 0.7613 (p) REVERT: B 78 THR cc_start: 0.8745 (t) cc_final: 0.8526 (m) REVERT: B 181 ASP cc_start: 0.6808 (m-30) cc_final: 0.6561 (m-30) REVERT: B 186 ASP cc_start: 0.6665 (p0) cc_final: 0.6326 (p0) REVERT: B 196 MET cc_start: 0.7045 (mmm) cc_final: 0.6799 (mmm) REVERT: B 208 ASN cc_start: 0.7158 (p0) cc_final: 0.6951 (p0) REVERT: B 232 TYR cc_start: 0.6768 (m-80) cc_final: 0.6327 (m-80) REVERT: C 14 VAL cc_start: 0.8476 (t) cc_final: 0.8161 (t) REVERT: C 52 LYS cc_start: 0.7848 (mtpp) cc_final: 0.7398 (mtpp) REVERT: C 91 ARG cc_start: 0.7918 (mmm160) cc_final: 0.6593 (tpt170) REVERT: C 95 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6170 (mm-30) REVERT: C 182 ASP cc_start: 0.5889 (p0) cc_final: 0.5278 (p0) REVERT: C 202 SER cc_start: 0.8470 (p) cc_final: 0.8187 (p) REVERT: C 214 VAL cc_start: 0.8278 (t) cc_final: 0.7928 (t) REVERT: D 64 ILE cc_start: 0.7151 (pt) cc_final: 0.6921 (pt) REVERT: D 104 ASP cc_start: 0.7330 (t0) cc_final: 0.7060 (t0) REVERT: D 121 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7346 (tm-30) REVERT: D 130 ARG cc_start: 0.8186 (ptt-90) cc_final: 0.7876 (ptt-90) REVERT: D 200 ILE cc_start: 0.8016 (pt) cc_final: 0.7499 (mm) REVERT: D 201 GLU cc_start: 0.5570 (mt-10) cc_final: 0.5365 (mt-10) REVERT: E 8 TYR cc_start: 0.7688 (m-10) cc_final: 0.6774 (m-80) REVERT: E 25 GLU cc_start: 0.6405 (tp30) cc_final: 0.5778 (tp30) REVERT: E 28 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7242 (mmm160) REVERT: E 53 ARG cc_start: 0.7949 (ptp-110) cc_final: 0.7703 (ptp-110) REVERT: E 186 ASP cc_start: 0.6037 (m-30) cc_final: 0.5137 (m-30) REVERT: E 234 GLU cc_start: 0.5284 (tp30) cc_final: 0.4941 (tp30) REVERT: F 9 ASP cc_start: 0.8416 (p0) cc_final: 0.7564 (p0) REVERT: F 52 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8620 (mtpp) REVERT: F 107 ILE cc_start: 0.9146 (tt) cc_final: 0.8895 (tt) REVERT: F 187 ASP cc_start: 0.5719 (m-30) cc_final: 0.5086 (m-30) REVERT: F 196 MET cc_start: 0.7371 (tpp) cc_final: 0.6965 (tpp) REVERT: G 41 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7782 (ttpt) REVERT: G 47 ILE cc_start: 0.8476 (mt) cc_final: 0.8257 (mt) REVERT: G 73 HIS cc_start: 0.7319 (p-80) cc_final: 0.6906 (p90) REVERT: G 89 ILE cc_start: 0.9251 (mm) cc_final: 0.8888 (mm) REVERT: G 191 LEU cc_start: 0.7551 (tp) cc_final: 0.7236 (tp) REVERT: G 198 LEU cc_start: 0.7822 (mt) cc_final: 0.7556 (mt) REVERT: G 211 VAL cc_start: 0.9152 (t) cc_final: 0.8774 (p) REVERT: G 234 GLU cc_start: 0.6317 (pp20) cc_final: 0.5754 (pp20) REVERT: 1 122 ILE cc_start: 0.7703 (mm) cc_final: 0.7422 (mm) REVERT: 1 123 TYR cc_start: 0.7788 (m-80) cc_final: 0.7554 (m-80) REVERT: 1 172 ILE cc_start: 0.6152 (mm) cc_final: 0.5313 (mm) REVERT: 1 173 TYR cc_start: 0.6059 (t80) cc_final: 0.5443 (t80) REVERT: 2 45 ILE cc_start: 0.7537 (tt) cc_final: 0.7133 (tt) REVERT: 2 48 ILE cc_start: 0.8377 (mm) cc_final: 0.8115 (mm) REVERT: 2 52 MET cc_start: 0.5863 (ttm) cc_final: 0.5505 (ttm) REVERT: 2 83 ARG cc_start: 0.7153 (ptm160) cc_final: 0.6696 (ptt180) REVERT: 3 46 TYR cc_start: 0.7268 (m-80) cc_final: 0.6773 (m-80) REVERT: 3 54 MET cc_start: 0.6913 (ttp) cc_final: 0.6544 (ttm) REVERT: 3 121 SER cc_start: 0.7710 (p) cc_final: 0.7389 (p) REVERT: 3 122 ILE cc_start: 0.8721 (mt) cc_final: 0.8492 (mt) REVERT: 4 48 ILE cc_start: 0.9213 (mm) cc_final: 0.8812 (mm) REVERT: 4 68 ARG cc_start: 0.8400 (tpp80) cc_final: 0.8149 (tpp80) REVERT: 4 87 VAL cc_start: 0.8375 (t) cc_final: 0.8035 (t) REVERT: 4 137 ILE cc_start: 0.8388 (mm) cc_final: 0.7732 (tt) REVERT: 4 191 ILE cc_start: 0.7699 (tp) cc_final: 0.7487 (tp) REVERT: 5 46 TYR cc_start: 0.7396 (m-80) cc_final: 0.7140 (m-10) REVERT: 5 92 THR cc_start: 0.8150 (p) cc_final: 0.7663 (p) REVERT: 5 146 THR cc_start: 0.6945 (p) cc_final: 0.6729 (p) REVERT: 5 204 VAL cc_start: 0.5791 (t) cc_final: 0.5551 (t) REVERT: 6 64 GLN cc_start: 0.6900 (pp30) cc_final: 0.5714 (pp30) REVERT: 7 81 ARG cc_start: 0.6347 (mtp180) cc_final: 0.5635 (mtp180) REVERT: 7 86 THR cc_start: 0.9025 (p) cc_final: 0.8799 (p) REVERT: 7 193 GLU cc_start: 0.5377 (tm-30) cc_final: 0.4776 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1189 average time/residue: 0.3516 time to fit residues: 650.0119 Evaluate side-chains 1104 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1104 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.7980 chunk 292 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 chunk 282 optimal weight: 0.9980 chunk 244 optimal weight: 0.0060 chunk 25 optimal weight: 0.2980 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 0.0670 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 75 ASN 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24968 Z= 0.244 Angle : 0.760 13.364 33660 Z= 0.402 Chirality : 0.049 0.286 3881 Planarity : 0.005 0.108 4329 Dihedral : 5.576 57.301 3498 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3122 helix: 0.30 (0.15), residues: 1190 sheet: 0.07 (0.19), residues: 622 loop : -1.28 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 73 PHE 0.032 0.002 PHE B 175 TYR 0.043 0.002 TYR 6 46 ARG 0.012 0.001 ARG 1 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1175 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8292 (tptp) cc_final: 0.7723 (mmmm) REVERT: A 71 ASP cc_start: 0.7319 (t0) cc_final: 0.7081 (t0) REVERT: A 130 ARG cc_start: 0.7848 (ptt90) cc_final: 0.7444 (ptt-90) REVERT: A 166 MET cc_start: 0.6996 (mtp) cc_final: 0.6795 (ttp) REVERT: A 208 ASN cc_start: 0.7724 (p0) cc_final: 0.7343 (p0) REVERT: A 211 VAL cc_start: 0.8221 (t) cc_final: 0.7593 (p) REVERT: B 6 MET cc_start: 0.6647 (pmm) cc_final: 0.5259 (ptp) REVERT: B 172 THR cc_start: 0.7057 (p) cc_final: 0.6772 (p) REVERT: B 181 ASP cc_start: 0.6707 (m-30) cc_final: 0.6483 (m-30) REVERT: B 186 ASP cc_start: 0.6703 (p0) cc_final: 0.6294 (p0) REVERT: B 214 VAL cc_start: 0.9337 (m) cc_final: 0.9025 (t) REVERT: C 12 ILE cc_start: 0.8736 (tp) cc_final: 0.8516 (tp) REVERT: C 14 VAL cc_start: 0.8419 (t) cc_final: 0.8120 (t) REVERT: C 52 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7418 (mtpp) REVERT: C 71 ASP cc_start: 0.8002 (t70) cc_final: 0.7729 (t70) REVERT: C 95 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6686 (mm-30) REVERT: C 164 ILE cc_start: 0.9239 (pt) cc_final: 0.9036 (pt) REVERT: C 182 ASP cc_start: 0.5884 (p0) cc_final: 0.5253 (p0) REVERT: C 196 MET cc_start: 0.6851 (tpp) cc_final: 0.6453 (tpp) REVERT: C 200 ILE cc_start: 0.8451 (pt) cc_final: 0.8181 (mt) REVERT: C 202 SER cc_start: 0.8467 (p) cc_final: 0.8030 (p) REVERT: C 214 VAL cc_start: 0.8374 (t) cc_final: 0.7903 (t) REVERT: D 121 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7280 (tm-30) REVERT: D 130 ARG cc_start: 0.8139 (ptt-90) cc_final: 0.7747 (ptt-90) REVERT: D 172 THR cc_start: 0.7858 (t) cc_final: 0.7625 (t) REVERT: D 200 ILE cc_start: 0.7899 (pt) cc_final: 0.7385 (mm) REVERT: E 8 TYR cc_start: 0.7613 (m-10) cc_final: 0.6631 (m-80) REVERT: E 25 GLU cc_start: 0.6367 (tp30) cc_final: 0.5782 (tp30) REVERT: E 28 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7193 (mmm160) REVERT: E 53 ARG cc_start: 0.7850 (ptp-110) cc_final: 0.7629 (ptp-110) REVERT: E 132 PHE cc_start: 0.8613 (m-80) cc_final: 0.8367 (m-10) REVERT: E 186 ASP cc_start: 0.5991 (m-30) cc_final: 0.5239 (m-30) REVERT: E 233 VAL cc_start: 0.7504 (t) cc_final: 0.7297 (t) REVERT: F 9 ASP cc_start: 0.8440 (p0) cc_final: 0.7591 (p0) REVERT: F 29 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6981 (mm-30) REVERT: F 107 ILE cc_start: 0.9027 (tt) cc_final: 0.8819 (tt) REVERT: F 196 MET cc_start: 0.7408 (tpp) cc_final: 0.7024 (tpp) REVERT: F 232 TYR cc_start: 0.7011 (m-10) cc_final: 0.6761 (m-10) REVERT: G 16 SER cc_start: 0.8497 (p) cc_final: 0.8142 (p) REVERT: G 41 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7694 (ttpt) REVERT: G 73 HIS cc_start: 0.7265 (p-80) cc_final: 0.6850 (p90) REVERT: G 89 ILE cc_start: 0.9207 (mm) cc_final: 0.8927 (mm) REVERT: G 174 PHE cc_start: 0.7359 (t80) cc_final: 0.7011 (t80) REVERT: G 181 ASP cc_start: 0.6168 (p0) cc_final: 0.5937 (p0) REVERT: G 191 LEU cc_start: 0.7560 (tp) cc_final: 0.7243 (tp) REVERT: G 211 VAL cc_start: 0.9242 (t) cc_final: 0.8891 (p) REVERT: G 234 GLU cc_start: 0.6266 (pp20) cc_final: 0.5712 (pp20) REVERT: 1 122 ILE cc_start: 0.7609 (mm) cc_final: 0.7277 (mm) REVERT: 1 172 ILE cc_start: 0.6008 (mm) cc_final: 0.5261 (mm) REVERT: 1 173 TYR cc_start: 0.6143 (t80) cc_final: 0.5424 (t80) REVERT: 2 45 ILE cc_start: 0.7404 (tt) cc_final: 0.6978 (tt) REVERT: 2 48 ILE cc_start: 0.8235 (mm) cc_final: 0.7991 (mm) REVERT: 2 83 ARG cc_start: 0.7143 (ptm160) cc_final: 0.6636 (ptt180) REVERT: 3 46 TYR cc_start: 0.7139 (m-80) cc_final: 0.6631 (m-80) REVERT: 3 54 MET cc_start: 0.6749 (ttp) cc_final: 0.6462 (ttm) REVERT: 3 87 VAL cc_start: 0.8279 (t) cc_final: 0.7714 (t) REVERT: 3 121 SER cc_start: 0.7725 (p) cc_final: 0.7359 (p) REVERT: 3 138 VAL cc_start: 0.7253 (p) cc_final: 0.6963 (p) REVERT: 3 162 ASP cc_start: 0.6145 (p0) cc_final: 0.5943 (p0) REVERT: 4 48 ILE cc_start: 0.9194 (mm) cc_final: 0.8781 (mm) REVERT: 4 54 MET cc_start: 0.7082 (tpp) cc_final: 0.6787 (tpp) REVERT: 4 137 ILE cc_start: 0.8329 (mm) cc_final: 0.7781 (mm) REVERT: 5 92 THR cc_start: 0.8051 (p) cc_final: 0.7798 (p) REVERT: 5 115 ILE cc_start: 0.7327 (pt) cc_final: 0.6982 (pt) REVERT: 5 142 SER cc_start: 0.6746 (t) cc_final: 0.6501 (t) REVERT: 5 146 THR cc_start: 0.6919 (p) cc_final: 0.6696 (p) REVERT: 5 191 ILE cc_start: 0.7285 (mt) cc_final: 0.7077 (mt) REVERT: 6 64 GLN cc_start: 0.6351 (pp30) cc_final: 0.5972 (pp30) REVERT: 6 68 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7503 (ttp-110) REVERT: 6 79 ILE cc_start: 0.9080 (mt) cc_final: 0.8134 (mt) REVERT: 6 80 ARG cc_start: 0.8786 (ttm110) cc_final: 0.8359 (mtt-85) REVERT: 7 193 GLU cc_start: 0.5247 (tm-30) cc_final: 0.4899 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1175 average time/residue: 0.3603 time to fit residues: 667.8240 Evaluate side-chains 1086 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1086 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 251 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 198 GLN ** 3 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 75 ASN 5 198 GLN 6 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.175553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.143208 restraints weight = 36665.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.147429 restraints weight = 21155.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.150272 restraints weight = 14302.344| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.8066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24968 Z= 0.296 Angle : 0.769 13.702 33660 Z= 0.408 Chirality : 0.049 0.294 3881 Planarity : 0.005 0.187 4329 Dihedral : 5.633 57.560 3498 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3122 helix: 0.31 (0.15), residues: 1180 sheet: 0.06 (0.19), residues: 621 loop : -1.35 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 73 PHE 0.026 0.002 PHE G 174 TYR 0.040 0.002 TYR 6 46 ARG 0.013 0.001 ARG B 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9843.69 seconds wall clock time: 173 minutes 48.98 seconds (10428.98 seconds total)