Starting phenix.real_space_refine on Wed Feb 14 12:40:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch6_30369/02_2024/7ch6_30369_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch6_30369/02_2024/7ch6_30369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch6_30369/02_2024/7ch6_30369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch6_30369/02_2024/7ch6_30369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch6_30369/02_2024/7ch6_30369_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch6_30369/02_2024/7ch6_30369_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 58 5.16 5 C 5934 2.51 5 N 1584 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.57 Number of scatterers: 9260 At special positions: 0 Unit cell: (105.04, 109.2, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 6 15.00 O 1678 8.00 N 1584 7.00 C 5934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 51.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 4.914A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.855A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 81 removed outlier: 3.756A pdb=" N LEU A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 61 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE A 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 66 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 69 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.902A pdb=" N GLY A 88 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA A 92 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.682A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 128 through 134 Processing helix chain 'A' and resid 139 through 174 removed outlier: 4.935A pdb=" N SER A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix removed outlier: 3.601A pdb=" N ILE A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.842A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 196 through 216 removed outlier: 3.778A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 258 removed outlier: 3.544A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 removed outlier: 4.914A pdb=" N THR B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.855A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 81 removed outlier: 3.755A pdb=" N LEU B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 60 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL B 61 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE B 65 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 66 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 69 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 71 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN B 73 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR B 75 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 76 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B 79 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 removed outlier: 3.902A pdb=" N GLY B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA B 92 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.683A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 128 through 134 Processing helix chain 'B' and resid 139 through 174 removed outlier: 4.934A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix removed outlier: 3.601A pdb=" N ILE B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) Proline residue: B 156 - end of helix removed outlier: 3.841A pdb=" N VAL B 160 " --> pdb=" O PRO B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 196 through 216 removed outlier: 3.778A pdb=" N LYS B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 258 removed outlier: 3.544A pdb=" N SER B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 Processing helix chain 'C' and resid 79 through 86 removed outlier: 4.138A pdb=" N ARG C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 3.662A pdb=" N TYR C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.575A pdb=" N SER C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.117A pdb=" N ARG C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 193 removed outlier: 3.628A pdb=" N ILE C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 removed outlier: 4.160A pdb=" N SER C 210 " --> pdb=" O PRO C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.978A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 79 through 86 removed outlier: 4.137A pdb=" N ARG D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 removed outlier: 3.662A pdb=" N TYR D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.576A pdb=" N SER D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 removed outlier: 4.117A pdb=" N ARG D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 removed outlier: 3.628A pdb=" N ILE D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 4.159A pdb=" N SER D 210 " --> pdb=" O PRO D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.977A pdb=" N PHE D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 265 No H-bonds generated for 'chain 'D' and resid 262 through 265' Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.917A pdb=" N GLU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU E 33 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.916A pdb=" N GLU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU F 33 " --> pdb=" O TRP F 29 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 67 Processing helix chain 'F' and resid 79 through 87 Processing sheet with id= A, first strand: chain 'C' and resid 214 through 217 removed outlier: 3.611A pdb=" N ALA C 38 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 199 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER C 88 " --> pdb=" O MET C 167 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP C 169 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 90 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.699A pdb=" N GLU C 64 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 214 through 217 removed outlier: 3.611A pdb=" N ALA D 38 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 199 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER D 88 " --> pdb=" O MET D 167 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP D 169 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU D 90 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.698A pdb=" N GLU D 64 " --> pdb=" O ARG D 12 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 5 through 9 Processing sheet with id= F, first strand: chain 'E' and resid 41 through 43 removed outlier: 6.123A pdb=" N THR E 73 " --> pdb=" O ILE E 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 5 through 9 Processing sheet with id= H, first strand: chain 'F' and resid 41 through 43 removed outlier: 6.123A pdb=" N THR F 73 " --> pdb=" O ILE F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 358 hydrogen bonds defined for protein. 972 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: 2.44 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3003 1.34 - 1.46: 1620 1.46 - 1.57: 4695 1.57 - 1.69: 10 1.69 - 1.81: 108 Bond restraints: 9436 Sorted by residual: bond pdb=" N3B ANP C 301 " pdb=" PG ANP C 301 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" O3A ANP C 301 " pdb=" PB ANP C 301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP D 301 " pdb=" PA ANP D 301 " ideal model delta sigma weight residual 1.655 1.602 0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 9431 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.37: 315 106.37 - 113.30: 5428 113.30 - 120.22: 3508 120.22 - 127.15: 3463 127.15 - 134.08: 120 Bond angle restraints: 12834 Sorted by residual: angle pdb=" C ASP C 204 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " ideal model delta sigma weight residual 120.43 124.33 -3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" C ASP D 204 " pdb=" N VAL D 205 " pdb=" CA VAL D 205 " ideal model delta sigma weight residual 120.43 124.33 -3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" C VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta sigma weight residual 113.70 110.36 3.34 9.50e-01 1.11e+00 1.24e+01 angle pdb=" C VAL D 205 " pdb=" CA VAL D 205 " pdb=" CB VAL D 205 " ideal model delta sigma weight residual 113.70 110.40 3.30 9.50e-01 1.11e+00 1.20e+01 angle pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " pdb=" O2G ANP D 301 " ideal model delta sigma weight residual 101.05 110.61 -9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 12829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 5261 23.78 - 47.56: 314 47.56 - 71.34: 78 71.34 - 95.12: 11 95.12 - 118.89: 4 Dihedral angle restraints: 5668 sinusoidal: 2228 harmonic: 3440 Sorted by residual: dihedral pdb=" CA LEU E 95 " pdb=" C LEU E 95 " pdb=" N PRO E 96 " pdb=" CA PRO E 96 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU F 95 " pdb=" C LEU F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA MET B 134 " pdb=" C MET B 134 " pdb=" N MET B 135 " pdb=" CA MET B 135 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.951: 1535 0.951 - 1.902: 0 1.902 - 2.853: 0 2.853 - 3.803: 0 3.803 - 4.754: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C1' ANP C 301 " pdb=" C2' ANP C 301 " pdb=" N9 ANP C 301 " pdb=" O4' ANP C 301 " both_signs ideal model delta sigma weight residual False 2.42 -2.33 4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C3' ANP C 301 " pdb=" C2' ANP C 301 " pdb=" C4' ANP C 301 " pdb=" O3' ANP C 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' ANP D 301 " pdb=" C2' ANP D 301 " pdb=" C4' ANP D 301 " pdb=" O3' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1533 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 95 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO E 96 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 95 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO F 96 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 41 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO B 42 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.021 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 180 2.64 - 3.21: 9206 3.21 - 3.77: 14692 3.77 - 4.34: 20266 4.34 - 4.90: 33344 Nonbonded interactions: 77688 Sorted by model distance: nonbonded pdb=" N3 ANP C 301 " pdb=" O2' ANP C 301 " model vdw 2.077 3.120 nonbonded pdb=" OG SER B 130 " pdb=" OE1 GLN C 57 " model vdw 2.104 2.440 nonbonded pdb=" OG SER A 228 " pdb=" OG SER B 228 " model vdw 2.117 2.440 nonbonded pdb=" OG SER A 131 " pdb=" NH2 ARG D 157 " model vdw 2.117 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 62 " model vdw 2.128 2.440 ... (remaining 77683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.010 Extract box with map and model: 4.080 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.050 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.008 0.165 9436 Z= 0.497 Angle : 0.821 9.587 12834 Z= 0.451 Chirality : 0.130 4.754 1536 Planarity : 0.006 0.118 1606 Dihedral : 16.465 118.895 3456 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 12.88 % Allowed : 11.87 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.20), residues: 1202 helix: -2.92 (0.15), residues: 650 sheet: -0.75 (0.94), residues: 40 loop : -3.21 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 195 HIS 0.004 0.001 HIS D 113 PHE 0.015 0.002 PHE A 162 TYR 0.011 0.002 TYR D 256 ARG 0.005 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 257 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 51 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 70 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 96 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 116 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7888 (mtm) REVERT: A 244 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 247 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 31 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8686 (mt) REVERT: B 70 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 96 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 116 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7382 (mp) REVERT: B 123 MET cc_start: 0.8040 (mtt) cc_final: 0.7769 (mtm) REVERT: B 244 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 247 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (mm) REVERT: C 170 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: C 176 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (p0) REVERT: C 178 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8872 (tt) REVERT: D 170 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: D 249 ASP cc_start: 0.7664 (t0) cc_final: 0.7358 (p0) REVERT: E 63 ASP cc_start: 0.7917 (t70) cc_final: 0.7700 (t70) REVERT: F 21 ASP cc_start: 0.8688 (p0) cc_final: 0.8117 (p0) REVERT: F 89 ASN cc_start: 0.8389 (t0) cc_final: 0.7832 (t0) outliers start: 128 outliers final: 47 residues processed: 356 average time/residue: 0.2155 time to fit residues: 104.5570 Evaluate side-chains 254 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 190 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 50 ASN A 190 GLN B 47 GLN B 50 ASN B 190 GLN C 214 HIS D 175 GLN D 214 HIS F 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9436 Z= 0.231 Angle : 0.708 9.639 12834 Z= 0.333 Chirality : 0.045 0.163 1536 Planarity : 0.006 0.107 1606 Dihedral : 12.730 89.071 1471 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 9.96 % Allowed : 17.51 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 1202 helix: -2.10 (0.17), residues: 650 sheet: -2.20 (0.59), residues: 78 loop : -2.63 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 7 HIS 0.005 0.001 HIS C 113 PHE 0.012 0.001 PHE D 91 TYR 0.012 0.001 TYR D 81 ARG 0.010 0.001 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 219 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 51 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8780 (t) REVERT: A 56 MET cc_start: 0.7544 (ttm) cc_final: 0.7276 (mtt) REVERT: A 70 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 89 MET cc_start: 0.7798 (ttp) cc_final: 0.7544 (ttt) REVERT: A 96 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 116 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 120 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8192 (pt) REVERT: A 123 MET cc_start: 0.7963 (mtt) cc_final: 0.7709 (mtm) REVERT: A 143 VAL cc_start: 0.9039 (t) cc_final: 0.8808 (p) REVERT: A 198 ASP cc_start: 0.7615 (t0) cc_final: 0.7331 (t0) REVERT: A 216 ILE cc_start: 0.8571 (pp) cc_final: 0.8153 (mm) REVERT: B 31 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 70 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8620 (tt) REVERT: B 96 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 120 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8187 (pt) REVERT: B 123 MET cc_start: 0.7903 (mtt) cc_final: 0.7642 (mtm) REVERT: B 143 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8881 (p) REVERT: C 172 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7964 (p90) REVERT: C 178 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8764 (tt) REVERT: C 207 GLU cc_start: 0.7835 (mp0) cc_final: 0.7578 (mp0) REVERT: D 172 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8018 (p90) REVERT: D 178 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8630 (tt) REVERT: D 249 ASP cc_start: 0.7670 (t0) cc_final: 0.7432 (p0) REVERT: E 89 ASN cc_start: 0.8308 (t0) cc_final: 0.7585 (t0) REVERT: F 22 GLN cc_start: 0.8289 (pp30) cc_final: 0.7910 (mp10) REVERT: F 66 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7850 (tppt) REVERT: F 89 ASN cc_start: 0.8260 (t0) cc_final: 0.7713 (t0) REVERT: F 93 ASP cc_start: 0.8427 (p0) cc_final: 0.8143 (p0) outliers start: 99 outliers final: 44 residues processed: 300 average time/residue: 0.2170 time to fit residues: 91.6247 Evaluate side-chains 253 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 194 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 ASN C 214 HIS D 175 GLN D 214 HIS E 60 HIS E 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.197 Angle : 0.642 9.660 12834 Z= 0.306 Chirality : 0.043 0.176 1536 Planarity : 0.005 0.101 1606 Dihedral : 10.478 80.291 1431 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 8.85 % Allowed : 19.42 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.23), residues: 1202 helix: -1.55 (0.19), residues: 650 sheet: -1.77 (0.68), residues: 58 loop : -2.39 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 7 HIS 0.003 0.001 HIS C 113 PHE 0.009 0.001 PHE B 162 TYR 0.013 0.001 TYR C 81 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 218 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8554 (mt) REVERT: A 51 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8810 (t) REVERT: A 56 MET cc_start: 0.7690 (ttm) cc_final: 0.7397 (mtt) REVERT: A 89 MET cc_start: 0.7684 (ttp) cc_final: 0.7368 (ttt) REVERT: A 96 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 116 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7471 (mp) REVERT: A 120 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.7955 (pt) REVERT: A 123 MET cc_start: 0.7853 (mtt) cc_final: 0.7637 (mtm) REVERT: A 133 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: A 143 VAL cc_start: 0.8955 (t) cc_final: 0.8659 (p) REVERT: A 216 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 31 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 70 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 120 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8043 (pt) REVERT: B 123 MET cc_start: 0.7838 (mtt) cc_final: 0.7607 (mtm) REVERT: B 128 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: C 207 GLU cc_start: 0.7860 (mp0) cc_final: 0.7653 (mp0) REVERT: D 172 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8100 (p90) REVERT: D 249 ASP cc_start: 0.7659 (t0) cc_final: 0.7412 (p0) REVERT: E 7 TRP cc_start: 0.8073 (p90) cc_final: 0.7598 (p-90) REVERT: E 22 GLN cc_start: 0.8227 (pp30) cc_final: 0.7824 (mp10) REVERT: E 66 LYS cc_start: 0.8218 (mmtm) cc_final: 0.8016 (tptt) REVERT: E 89 ASN cc_start: 0.8333 (t0) cc_final: 0.7689 (t0) REVERT: E 93 ASP cc_start: 0.8479 (p0) cc_final: 0.8222 (p0) REVERT: F 7 TRP cc_start: 0.8105 (p90) cc_final: 0.7440 (p-90) REVERT: F 22 GLN cc_start: 0.8203 (pp30) cc_final: 0.7846 (mp10) REVERT: F 23 ASP cc_start: 0.7884 (t0) cc_final: 0.7567 (t0) REVERT: F 89 ASN cc_start: 0.8295 (t0) cc_final: 0.7762 (t0) REVERT: F 93 ASP cc_start: 0.8387 (p0) cc_final: 0.8116 (p0) outliers start: 88 outliers final: 54 residues processed: 287 average time/residue: 0.1925 time to fit residues: 77.5092 Evaluate side-chains 265 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 199 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 HIS C 214 HIS D 175 GLN D 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9436 Z= 0.302 Angle : 0.674 10.914 12834 Z= 0.320 Chirality : 0.045 0.145 1536 Planarity : 0.006 0.110 1606 Dihedral : 10.072 80.557 1423 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 9.76 % Allowed : 19.22 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.23), residues: 1202 helix: -1.39 (0.19), residues: 654 sheet: -1.52 (0.53), residues: 92 loop : -2.29 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 7 HIS 0.004 0.001 HIS C 62 PHE 0.011 0.001 PHE A 162 TYR 0.010 0.001 TYR D 81 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 201 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 56 MET cc_start: 0.7820 (ttm) cc_final: 0.7565 (mtt) REVERT: A 116 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7402 (mp) REVERT: A 120 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8119 (pt) REVERT: A 123 MET cc_start: 0.7925 (mtt) cc_final: 0.7706 (mtm) REVERT: A 128 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 133 GLU cc_start: 0.7685 (tt0) cc_final: 0.7429 (tt0) REVERT: A 216 ILE cc_start: 0.8675 (pp) cc_final: 0.8299 (mm) REVERT: B 31 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8626 (mt) REVERT: B 120 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8131 (pt) REVERT: B 123 MET cc_start: 0.7909 (mtt) cc_final: 0.7664 (mtm) REVERT: B 128 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: C 170 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: D 170 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: D 249 ASP cc_start: 0.7686 (t0) cc_final: 0.7430 (p0) REVERT: E 7 TRP cc_start: 0.8113 (p90) cc_final: 0.7517 (p-90) REVERT: E 66 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8070 (tptt) REVERT: E 68 GLN cc_start: 0.8010 (pm20) cc_final: 0.7563 (pm20) REVERT: E 89 ASN cc_start: 0.8348 (t0) cc_final: 0.7683 (t0) REVERT: E 93 ASP cc_start: 0.8479 (p0) cc_final: 0.8204 (p0) REVERT: F 7 TRP cc_start: 0.8120 (p90) cc_final: 0.7330 (p-90) REVERT: F 89 ASN cc_start: 0.8292 (t0) cc_final: 0.7720 (t0) REVERT: F 93 ASP cc_start: 0.8419 (p0) cc_final: 0.8152 (p0) outliers start: 97 outliers final: 70 residues processed: 280 average time/residue: 0.2044 time to fit residues: 80.4542 Evaluate side-chains 272 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 193 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 HIS C 214 HIS D 214 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9436 Z= 0.303 Angle : 0.667 9.871 12834 Z= 0.318 Chirality : 0.045 0.156 1536 Planarity : 0.006 0.109 1606 Dihedral : 9.970 79.661 1422 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 9.86 % Allowed : 19.72 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1202 helix: -1.28 (0.19), residues: 652 sheet: -1.54 (0.52), residues: 92 loop : -2.25 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 7 HIS 0.007 0.001 HIS D 113 PHE 0.012 0.001 PHE B 162 TYR 0.007 0.001 TYR C 256 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 201 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8559 (mt) REVERT: A 56 MET cc_start: 0.7834 (ttm) cc_final: 0.7573 (mtt) REVERT: A 116 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 120 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8076 (pt) REVERT: A 123 MET cc_start: 0.7947 (mtt) cc_final: 0.7735 (mtm) REVERT: A 128 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: A 133 GLU cc_start: 0.7717 (tt0) cc_final: 0.7487 (tt0) REVERT: A 216 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8260 (mm) REVERT: B 31 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 120 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8118 (pt) REVERT: B 123 MET cc_start: 0.7938 (mtt) cc_final: 0.7729 (mtm) REVERT: B 128 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 133 GLU cc_start: 0.7714 (tt0) cc_final: 0.7492 (tt0) REVERT: C 170 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: C 178 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (tt) REVERT: C 207 GLU cc_start: 0.8127 (mp0) cc_final: 0.7524 (mp0) REVERT: D 51 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8024 (mp) REVERT: D 170 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: D 172 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8272 (p90) REVERT: D 249 ASP cc_start: 0.7678 (t0) cc_final: 0.7452 (p0) REVERT: E 7 TRP cc_start: 0.8130 (p90) cc_final: 0.7471 (p-90) REVERT: E 22 GLN cc_start: 0.8264 (pp30) cc_final: 0.7827 (mp10) REVERT: E 66 LYS cc_start: 0.8258 (mmtm) cc_final: 0.8045 (tptt) REVERT: E 68 GLN cc_start: 0.7924 (pm20) cc_final: 0.7506 (pm20) REVERT: E 89 ASN cc_start: 0.8358 (t0) cc_final: 0.7686 (t0) REVERT: E 93 ASP cc_start: 0.8500 (p0) cc_final: 0.8217 (p0) REVERT: F 22 GLN cc_start: 0.8340 (pp30) cc_final: 0.7974 (mp10) REVERT: F 23 ASP cc_start: 0.7754 (t0) cc_final: 0.7469 (t0) REVERT: F 89 ASN cc_start: 0.8286 (t0) cc_final: 0.8010 (t0) REVERT: F 93 ASP cc_start: 0.8439 (p0) cc_final: 0.8210 (p0) outliers start: 98 outliers final: 67 residues processed: 281 average time/residue: 0.1977 time to fit residues: 78.2555 Evaluate side-chains 272 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 192 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN C 62 HIS C 214 HIS D 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9436 Z= 0.199 Angle : 0.622 9.737 12834 Z= 0.297 Chirality : 0.042 0.143 1536 Planarity : 0.005 0.103 1606 Dihedral : 9.453 72.939 1420 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.35 % Allowed : 22.43 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1202 helix: -0.91 (0.20), residues: 640 sheet: -1.38 (0.54), residues: 92 loop : -2.13 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 7 HIS 0.006 0.001 HIS D 113 PHE 0.009 0.001 PHE A 162 TYR 0.007 0.001 TYR C 261 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 206 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (mt) REVERT: A 56 MET cc_start: 0.7782 (ttm) cc_final: 0.7538 (mtt) REVERT: A 120 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.7949 (pt) REVERT: A 123 MET cc_start: 0.7868 (mtt) cc_final: 0.7650 (mtm) REVERT: A 128 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 133 GLU cc_start: 0.7650 (tt0) cc_final: 0.7431 (tt0) REVERT: A 134 MET cc_start: 0.8793 (tpt) cc_final: 0.8442 (tpt) REVERT: A 216 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8285 (mm) REVERT: B 31 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8517 (mt) REVERT: B 120 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.7895 (pt) REVERT: B 123 MET cc_start: 0.7840 (mtt) cc_final: 0.7630 (mtm) REVERT: B 128 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: C 172 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8164 (p90) REVERT: C 178 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8813 (tt) REVERT: C 207 GLU cc_start: 0.8040 (mp0) cc_final: 0.7376 (mp0) REVERT: D 51 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8004 (mp) REVERT: D 172 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8288 (p90) REVERT: E 7 TRP cc_start: 0.8099 (p90) cc_final: 0.7515 (p-90) REVERT: E 22 GLN cc_start: 0.8258 (pp30) cc_final: 0.7890 (mp10) REVERT: E 66 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7975 (tptt) REVERT: E 89 ASN cc_start: 0.8354 (t0) cc_final: 0.7670 (t0) REVERT: E 93 ASP cc_start: 0.8468 (p0) cc_final: 0.8194 (p0) REVERT: F 22 GLN cc_start: 0.8247 (pp30) cc_final: 0.7965 (mp10) REVERT: F 23 ASP cc_start: 0.7757 (t0) cc_final: 0.7541 (t0) REVERT: F 89 ASN cc_start: 0.8287 (t0) cc_final: 0.7752 (t0) REVERT: F 93 ASP cc_start: 0.8446 (p0) cc_final: 0.8226 (p0) outliers start: 83 outliers final: 53 residues processed: 269 average time/residue: 0.1986 time to fit residues: 74.3116 Evaluate side-chains 265 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 201 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 52 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: C 62 HIS ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 262 HIS D 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9436 Z= 0.205 Angle : 0.632 9.686 12834 Z= 0.303 Chirality : 0.043 0.202 1536 Planarity : 0.005 0.100 1606 Dihedral : 8.854 67.523 1410 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 7.24 % Allowed : 23.84 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.24), residues: 1202 helix: -0.84 (0.20), residues: 650 sheet: -0.97 (0.60), residues: 80 loop : -2.04 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 7 HIS 0.006 0.001 HIS C 62 PHE 0.009 0.001 PHE A 162 TYR 0.007 0.001 TYR C 81 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 206 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 56 MET cc_start: 0.7741 (ttm) cc_final: 0.7500 (mtt) REVERT: A 120 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.7971 (pt) REVERT: A 123 MET cc_start: 0.7835 (mtt) cc_final: 0.7630 (mtm) REVERT: A 128 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 134 MET cc_start: 0.8766 (tpt) cc_final: 0.8473 (tpt) REVERT: A 197 MET cc_start: 0.7339 (tpp) cc_final: 0.7060 (tpp) REVERT: A 216 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 31 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 120 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.7919 (pt) REVERT: B 123 MET cc_start: 0.7826 (mtt) cc_final: 0.7617 (mtm) REVERT: B 128 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: B 197 MET cc_start: 0.7038 (tpp) cc_final: 0.6795 (tpp) REVERT: C 170 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: C 172 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8212 (p90) REVERT: C 178 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8827 (tt) REVERT: C 207 GLU cc_start: 0.8021 (mp0) cc_final: 0.7619 (mp0) REVERT: D 51 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8036 (mp) REVERT: D 170 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: D 172 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8452 (p90) REVERT: E 7 TRP cc_start: 0.8101 (p90) cc_final: 0.7523 (p-90) REVERT: E 22 GLN cc_start: 0.8171 (pp30) cc_final: 0.7910 (mp10) REVERT: E 66 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7889 (tptt) REVERT: E 89 ASN cc_start: 0.8364 (t0) cc_final: 0.7708 (t0) REVERT: E 93 ASP cc_start: 0.8451 (p0) cc_final: 0.8171 (p0) REVERT: F 22 GLN cc_start: 0.8201 (pp30) cc_final: 0.7992 (mp10) REVERT: F 23 ASP cc_start: 0.7720 (t0) cc_final: 0.7496 (t0) REVERT: F 89 ASN cc_start: 0.8303 (t0) cc_final: 0.7819 (t0) REVERT: F 93 ASP cc_start: 0.8430 (p0) cc_final: 0.8189 (p0) outliers start: 72 outliers final: 47 residues processed: 256 average time/residue: 0.2072 time to fit residues: 73.2122 Evaluate side-chains 259 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 199 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.0050 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 103 optimal weight: 0.0070 overall best weight: 0.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 HIS ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9436 Z= 0.170 Angle : 0.623 9.498 12834 Z= 0.298 Chirality : 0.041 0.168 1536 Planarity : 0.005 0.093 1606 Dihedral : 8.062 60.248 1403 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.84 % Allowed : 25.96 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1202 helix: -0.58 (0.21), residues: 646 sheet: -1.10 (0.63), residues: 70 loop : -1.87 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 7 HIS 0.006 0.001 HIS C 62 PHE 0.007 0.001 PHE C 172 TYR 0.005 0.001 TYR C 81 ARG 0.007 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 1.124 Fit side-chains REVERT: A 31 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 56 MET cc_start: 0.7693 (ttm) cc_final: 0.7451 (mtt) REVERT: A 120 ILE cc_start: 0.8416 (pt) cc_final: 0.7954 (pt) REVERT: A 123 MET cc_start: 0.7807 (mtt) cc_final: 0.7563 (mtm) REVERT: A 134 MET cc_start: 0.8677 (tpt) cc_final: 0.8448 (tpt) REVERT: A 201 ASN cc_start: 0.7646 (m-40) cc_final: 0.7360 (m-40) REVERT: A 216 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8284 (mm) REVERT: B 31 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 123 MET cc_start: 0.7746 (mtt) cc_final: 0.7537 (mtm) REVERT: C 172 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8267 (p90) REVERT: C 178 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8833 (tt) REVERT: C 207 GLU cc_start: 0.7908 (mp0) cc_final: 0.7516 (mp0) REVERT: C 262 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.6211 (m-70) REVERT: D 51 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8029 (mp) REVERT: E 7 TRP cc_start: 0.8108 (p90) cc_final: 0.7577 (p-90) REVERT: E 66 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7776 (tptt) REVERT: E 89 ASN cc_start: 0.8342 (t0) cc_final: 0.7752 (t0) REVERT: F 89 ASN cc_start: 0.8371 (t0) cc_final: 0.7912 (t0) REVERT: F 93 ASP cc_start: 0.8493 (p0) cc_final: 0.8210 (p0) outliers start: 58 outliers final: 42 residues processed: 256 average time/residue: 0.2094 time to fit residues: 74.3501 Evaluate side-chains 248 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN C 62 HIS C 71 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 214 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9436 Z= 0.200 Angle : 0.625 9.597 12834 Z= 0.300 Chirality : 0.042 0.180 1536 Planarity : 0.005 0.097 1606 Dihedral : 7.861 59.671 1394 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.84 % Allowed : 26.66 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1202 helix: -0.49 (0.21), residues: 648 sheet: -1.12 (0.63), residues: 70 loop : -1.91 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 7 HIS 0.006 0.001 HIS C 62 PHE 0.009 0.001 PHE A 162 TYR 0.004 0.001 TYR C 108 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 204 time to evaluate : 1.139 Fit side-chains REVERT: A 56 MET cc_start: 0.7764 (ttm) cc_final: 0.7530 (mtt) REVERT: A 120 ILE cc_start: 0.8424 (pt) cc_final: 0.7866 (pt) REVERT: A 123 MET cc_start: 0.7827 (mtt) cc_final: 0.7588 (mtm) REVERT: A 134 MET cc_start: 0.8689 (tpt) cc_final: 0.8445 (tpt) REVERT: A 201 ASN cc_start: 0.7644 (m-40) cc_final: 0.7374 (m-40) REVERT: A 216 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8296 (mm) REVERT: B 31 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 123 MET cc_start: 0.7805 (mtt) cc_final: 0.7550 (mtm) REVERT: B 257 MET cc_start: 0.7358 (mtm) cc_final: 0.7125 (mtp) REVERT: C 75 MET cc_start: 0.7329 (mtt) cc_final: 0.7123 (mtt) REVERT: C 172 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8299 (p90) REVERT: C 178 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 207 GLU cc_start: 0.7937 (mp0) cc_final: 0.7574 (mp0) REVERT: C 262 HIS cc_start: 0.6426 (OUTLIER) cc_final: 0.6204 (m-70) REVERT: D 51 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7959 (mp) REVERT: D 170 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: E 7 TRP cc_start: 0.8078 (p90) cc_final: 0.7552 (p-90) REVERT: E 66 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7786 (tptt) REVERT: E 89 ASN cc_start: 0.8329 (t0) cc_final: 0.7736 (t0) REVERT: F 89 ASN cc_start: 0.8379 (t0) cc_final: 0.7908 (t0) REVERT: F 93 ASP cc_start: 0.8479 (p0) cc_final: 0.8201 (p0) outliers start: 58 outliers final: 45 residues processed: 246 average time/residue: 0.2172 time to fit residues: 74.0993 Evaluate side-chains 251 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN C 71 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS D 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9436 Z= 0.223 Angle : 0.665 9.654 12834 Z= 0.318 Chirality : 0.043 0.183 1536 Planarity : 0.005 0.097 1606 Dihedral : 7.872 59.265 1393 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.43 % Allowed : 26.86 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1202 helix: -0.44 (0.21), residues: 658 sheet: -1.14 (0.63), residues: 70 loop : -1.91 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 7 HIS 0.007 0.001 HIS C 62 PHE 0.009 0.001 PHE A 162 TYR 0.009 0.001 TYR C 81 ARG 0.007 0.000 ARG F 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 199 time to evaluate : 1.147 Fit side-chains REVERT: A 56 MET cc_start: 0.7774 (ttm) cc_final: 0.7528 (mtt) REVERT: A 120 ILE cc_start: 0.8449 (pt) cc_final: 0.7883 (pt) REVERT: A 123 MET cc_start: 0.7843 (mtt) cc_final: 0.7599 (mtm) REVERT: A 134 MET cc_start: 0.8657 (tpt) cc_final: 0.8431 (tpt) REVERT: A 189 MET cc_start: 0.6549 (tpp) cc_final: 0.6261 (tpt) REVERT: A 201 ASN cc_start: 0.7646 (m-40) cc_final: 0.7404 (m-40) REVERT: A 216 ILE cc_start: 0.8587 (pp) cc_final: 0.8298 (mm) REVERT: B 31 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 123 MET cc_start: 0.7830 (mtt) cc_final: 0.7572 (mtm) REVERT: C 172 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8233 (p90) REVERT: C 178 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 262 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.6306 (m-70) REVERT: D 51 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (mp) REVERT: D 170 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: E 7 TRP cc_start: 0.8093 (p90) cc_final: 0.7576 (p-90) REVERT: E 66 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7779 (tptt) REVERT: E 89 ASN cc_start: 0.8331 (t0) cc_final: 0.7725 (t0) REVERT: F 89 ASN cc_start: 0.8380 (t0) cc_final: 0.7896 (t0) REVERT: F 93 ASP cc_start: 0.8483 (p0) cc_final: 0.8194 (p0) outliers start: 54 outliers final: 45 residues processed: 238 average time/residue: 0.2138 time to fit residues: 70.1822 Evaluate side-chains 248 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 197 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 HIS ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103616 restraints weight = 13588.738| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.94 r_work: 0.3129 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9436 Z= 0.226 Angle : 0.655 9.615 12834 Z= 0.316 Chirality : 0.043 0.185 1536 Planarity : 0.005 0.098 1606 Dihedral : 7.874 59.406 1393 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.73 % Allowed : 26.96 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.25), residues: 1202 helix: -0.44 (0.21), residues: 658 sheet: -1.20 (0.62), residues: 70 loop : -1.88 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 7 HIS 0.005 0.001 HIS D 62 PHE 0.010 0.001 PHE D 91 TYR 0.010 0.001 TYR C 81 ARG 0.007 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2484.51 seconds wall clock time: 45 minutes 35.99 seconds (2735.99 seconds total)