Starting phenix.real_space_refine on Mon Mar 11 11:57:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8l_24896/03_2024/7s8l_24896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8l_24896/03_2024/7s8l_24896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8l_24896/03_2024/7s8l_24896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8l_24896/03_2024/7s8l_24896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8l_24896/03_2024/7s8l_24896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8l_24896/03_2024/7s8l_24896.pdb" } resolution = 2.45 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5244 2.51 5 N 1388 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 164": "OE1" <-> "OE2" Residue "R PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8177 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1862 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 8, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2475 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 4.67, per 1000 atoms: 0.57 Number of scatterers: 8177 At special positions: 0 Unit cell: (90.09, 122.85, 126.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1492 8.00 N 1388 7.00 C 5244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.854A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE R 57 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.826A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.881A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 167 removed outlier: 3.712A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 211 Processing helix chain 'R' and resid 219 through 245 Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.045A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.718A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.070A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.698A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.582A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.876A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 22 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.916A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.701A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.572A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 4.136A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.512A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.932A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 72 through 76 removed outlier: 3.995A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 3.865A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.899A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.934A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.824A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.776A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.922A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.560A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.988A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.410A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.410A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 148 411 hydrogen bonds defined for protein. 1149 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: 2.28 Time building geometry restraints manager: 3.11 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: 2623 1.34 - 1.46: 2027 1.46 - 1.58: 3631 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8353 Sorted by residual: bond pdb=" N CYS B 217 " pdb=" CA CYS B 217 " ideal model delta sigma weight residual 1.459 1.492 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.23e+00 bond pdb=" N THR B 216 " pdb=" CA THR B 216 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.44e-02 4.82e+03 6.62e+00 bond pdb=" N ALA B 218 " pdb=" CA ALA B 218 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.37e-02 5.33e+03 6.14e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.30e-02 5.92e+03 5.77e+00 ... (remaining 8348 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 177 106.72 - 113.54: 4580 113.54 - 120.36: 3016 120.36 - 127.18: 3510 127.18 - 134.01: 90 Bond angle restraints: 11373 Sorted by residual: angle pdb=" CA THR B 216 " pdb=" C THR B 216 " pdb=" O THR B 216 " ideal model delta sigma weight residual 121.49 117.46 4.03 1.16e+00 7.43e-01 1.21e+01 angle pdb=" CA CYS B 217 " pdb=" C CYS B 217 " pdb=" O CYS B 217 " ideal model delta sigma weight residual 119.08 116.08 3.00 1.05e+00 9.07e-01 8.17e+00 angle pdb=" N THR B 221 " pdb=" CA THR B 221 " pdb=" C THR B 221 " ideal model delta sigma weight residual 113.61 109.60 4.01 1.50e+00 4.44e-01 7.13e+00 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 109.81 115.53 -5.72 2.21e+00 2.05e-01 6.70e+00 angle pdb=" C GLY E 197 " pdb=" N THR E 198 " pdb=" CA THR E 198 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.37e+00 ... (remaining 11368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 4376 15.06 - 30.12: 369 30.12 - 45.17: 90 45.17 - 60.23: 15 60.23 - 75.29: 3 Dihedral angle restraints: 4853 sinusoidal: 1691 harmonic: 3162 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 141.50 -48.50 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP B 199 " pdb=" C ASP B 199 " pdb=" N ILE B 200 " pdb=" CA ILE B 200 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 979 0.042 - 0.083: 249 0.083 - 0.125: 94 0.125 - 0.166: 6 0.166 - 0.208: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1326 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 233 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU R 233 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU R 233 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 234 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 172 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO E 173 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 48 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" CG ASP D 48 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP D 48 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP D 48 " -0.009 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1369 2.77 - 3.30: 7110 3.30 - 3.84: 12625 3.84 - 4.37: 14156 4.37 - 4.90: 26477 Nonbonded interactions: 61737 Sorted by model distance: nonbonded pdb=" ND2 ASN R 48 " pdb=" OD2 ASP R 75 " model vdw 2.238 2.520 nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.324 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.333 2.440 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.340 2.520 ... (remaining 61732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 3.800 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.003 0.037 8353 Z= 0.177 Angle : 0.558 8.294 11373 Z= 0.317 Chirality : 0.042 0.208 1329 Planarity : 0.003 0.039 1430 Dihedral : 12.220 75.290 2805 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.27 (0.26), residues: 1074 helix: 3.16 (0.28), residues: 352 sheet: 0.62 (0.31), residues: 267 loop : -0.94 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 190 HIS 0.004 0.001 HIS C 54 PHE 0.017 0.001 PHE R 81 TYR 0.010 0.001 TYR E 178 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.930 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 177 average time/residue: 1.1358 time to fit residues: 213.4327 Evaluate side-chains 165 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 43 optimal weight: 0.0050 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.0000 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 116 ASN B 144 ASN C 35 ASN C 239 ASN E 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8353 Z= 0.138 Angle : 0.508 5.760 11373 Z= 0.274 Chirality : 0.041 0.150 1329 Planarity : 0.004 0.037 1430 Dihedral : 3.828 17.012 1168 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.94 % Allowed : 9.36 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.43 (0.26), residues: 1074 helix: 3.26 (0.28), residues: 355 sheet: 0.68 (0.30), residues: 279 loop : -0.88 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 96 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE R 81 TYR 0.017 0.001 TYR E 178 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 0.922 Fit side-chains REVERT: R 77 LEU cc_start: 0.7541 (mp) cc_final: 0.7341 (mp) REVERT: B 127 SER cc_start: 0.8575 (p) cc_final: 0.8344 (p) REVERT: B 130 ASN cc_start: 0.8759 (m110) cc_final: 0.8541 (m110) outliers start: 16 outliers final: 7 residues processed: 166 average time/residue: 1.1379 time to fit residues: 200.6783 Evaluate side-chains 165 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 35 ASN C 75 GLN C 88 ASN C 220 GLN C 237 ASN E 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8353 Z= 0.336 Angle : 0.659 6.407 11373 Z= 0.354 Chirality : 0.046 0.151 1329 Planarity : 0.004 0.050 1430 Dihedral : 4.436 19.177 1168 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.31 % Allowed : 11.91 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.12 (0.26), residues: 1074 helix: 2.88 (0.28), residues: 355 sheet: 0.67 (0.30), residues: 277 loop : -1.05 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 190 HIS 0.008 0.002 HIS E 35 PHE 0.016 0.002 PHE C 151 TYR 0.015 0.002 TYR E 95 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.956 Fit side-chains REVERT: R 280 PHE cc_start: 0.8308 (t80) cc_final: 0.8098 (t80) REVERT: B 127 SER cc_start: 0.8501 (p) cc_final: 0.8282 (p) REVERT: C 304 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7595 (mtm180) outliers start: 19 outliers final: 11 residues processed: 164 average time/residue: 1.2819 time to fit residues: 223.3188 Evaluate side-chains 173 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 128 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.0040 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 116 ASN B 244 ASN C 54 HIS C 88 ASN C 220 GLN E 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8353 Z= 0.245 Angle : 0.585 5.859 11373 Z= 0.316 Chirality : 0.043 0.145 1329 Planarity : 0.004 0.049 1430 Dihedral : 4.269 19.492 1166 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.52 % Allowed : 13.00 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.18 (0.26), residues: 1074 helix: 2.97 (0.28), residues: 355 sheet: 0.82 (0.30), residues: 270 loop : -1.13 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 190 HIS 0.006 0.001 HIS E 35 PHE 0.014 0.002 PHE C 234 TYR 0.013 0.002 TYR E 178 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 0.802 Fit side-chains REVERT: R 280 PHE cc_start: 0.8309 (t80) cc_final: 0.8101 (t80) REVERT: B 127 SER cc_start: 0.8481 (p) cc_final: 0.8264 (p) REVERT: C 304 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7580 (mtm180) REVERT: E 212 VAL cc_start: 0.8808 (m) cc_final: 0.8569 (t) outliers start: 29 outliers final: 16 residues processed: 175 average time/residue: 1.1221 time to fit residues: 209.1360 Evaluate side-chains 185 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 116 ASN B 229 ASN B 244 ASN C 75 GLN C 88 ASN C 220 GLN E 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8353 Z= 0.270 Angle : 0.609 9.499 11373 Z= 0.327 Chirality : 0.044 0.223 1329 Planarity : 0.004 0.051 1430 Dihedral : 4.396 28.006 1166 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.77 % Allowed : 13.24 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.15 (0.26), residues: 1074 helix: 2.92 (0.28), residues: 353 sheet: 0.91 (0.30), residues: 270 loop : -1.18 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 190 HIS 0.006 0.001 HIS E 35 PHE 0.014 0.002 PHE C 151 TYR 0.013 0.002 TYR B 163 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.007 Fit side-chains REVERT: R 280 PHE cc_start: 0.8312 (t80) cc_final: 0.8103 (t80) REVERT: B 127 SER cc_start: 0.8471 (p) cc_final: 0.8261 (p) REVERT: C 304 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7581 (mtm180) REVERT: E 128 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7223 (mtm) outliers start: 31 outliers final: 18 residues processed: 176 average time/residue: 1.0962 time to fit residues: 205.5259 Evaluate side-chains 186 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 244 ASN C 75 GLN C 88 ASN C 220 GLN E 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.217 Angle : 0.569 7.817 11373 Z= 0.308 Chirality : 0.043 0.208 1329 Planarity : 0.004 0.050 1430 Dihedral : 4.277 26.861 1166 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.04 % Allowed : 15.80 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.26), residues: 1074 helix: 3.05 (0.28), residues: 353 sheet: 0.97 (0.30), residues: 270 loop : -1.16 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 190 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 0.856 Fit side-chains REVERT: R 280 PHE cc_start: 0.8311 (t80) cc_final: 0.8108 (t80) REVERT: B 127 SER cc_start: 0.8470 (p) cc_final: 0.8252 (p) REVERT: C 304 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7565 (mtm180) outliers start: 25 outliers final: 18 residues processed: 174 average time/residue: 1.1440 time to fit residues: 211.4520 Evaluate side-chains 183 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 75 GLN C 88 ASN C 220 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8353 Z= 0.263 Angle : 0.605 7.395 11373 Z= 0.327 Chirality : 0.044 0.205 1329 Planarity : 0.004 0.052 1430 Dihedral : 4.396 28.396 1166 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.16 % Allowed : 15.80 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.22 (0.26), residues: 1074 helix: 2.98 (0.28), residues: 353 sheet: 0.98 (0.31), residues: 270 loop : -1.17 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 63 HIS 0.006 0.001 HIS E 35 PHE 0.014 0.002 PHE C 151 TYR 0.017 0.002 TYR B 163 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.886 Fit side-chains REVERT: B 127 SER cc_start: 0.8461 (p) cc_final: 0.8243 (p) REVERT: C 304 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7575 (mtm180) REVERT: E 6 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7914 (mp0) REVERT: E 93 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8169 (ttp) outliers start: 26 outliers final: 18 residues processed: 173 average time/residue: 1.0787 time to fit residues: 198.8947 Evaluate side-chains 186 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 244 ASN C 220 GLN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8353 Z= 0.216 Angle : 0.569 6.719 11373 Z= 0.308 Chirality : 0.043 0.193 1329 Planarity : 0.004 0.050 1430 Dihedral : 4.267 26.340 1166 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.92 % Allowed : 16.52 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.30 (0.26), residues: 1074 helix: 3.09 (0.28), residues: 353 sheet: 1.00 (0.30), residues: 270 loop : -1.15 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE R 280 TYR 0.016 0.001 TYR B 163 ARG 0.013 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 0.932 Fit side-chains REVERT: B 101 ASN cc_start: 0.7761 (t0) cc_final: 0.7526 (t0) REVERT: B 127 SER cc_start: 0.8471 (p) cc_final: 0.8239 (p) REVERT: C 254 ASP cc_start: 0.7302 (t70) cc_final: 0.7059 (t70) REVERT: C 304 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7564 (mtm180) REVERT: E 93 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8134 (ttp) outliers start: 24 outliers final: 19 residues processed: 170 average time/residue: 1.1555 time to fit residues: 208.9990 Evaluate side-chains 184 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 75 GLN C 88 ASN C 220 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8353 Z= 0.194 Angle : 0.556 7.592 11373 Z= 0.301 Chirality : 0.042 0.182 1329 Planarity : 0.004 0.049 1430 Dihedral : 4.171 25.122 1166 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 16.65 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.37 (0.26), residues: 1074 helix: 3.20 (0.27), residues: 353 sheet: 0.97 (0.30), residues: 271 loop : -1.11 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.005 0.001 HIS B 82 PHE 0.024 0.001 PHE R 280 TYR 0.014 0.001 TYR B 163 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 0.858 Fit side-chains REVERT: B 127 SER cc_start: 0.8476 (p) cc_final: 0.8239 (p) REVERT: C 254 ASP cc_start: 0.7281 (t70) cc_final: 0.7004 (t70) REVERT: E 93 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8151 (ttp) outliers start: 24 outliers final: 18 residues processed: 171 average time/residue: 1.1070 time to fit residues: 201.4728 Evaluate side-chains 177 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 88 ASN C 220 GLN D 18 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8353 Z= 0.333 Angle : 0.660 8.898 11373 Z= 0.355 Chirality : 0.046 0.201 1329 Planarity : 0.005 0.054 1430 Dihedral : 4.555 29.208 1166 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.79 % Allowed : 16.77 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.14 (0.26), residues: 1074 helix: 2.91 (0.28), residues: 353 sheet: 0.91 (0.30), residues: 275 loop : -1.20 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 63 HIS 0.008 0.002 HIS E 35 PHE 0.022 0.002 PHE R 280 TYR 0.023 0.002 TYR B 163 ARG 0.013 0.000 ARG B 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 0.823 Fit side-chains REVERT: B 127 SER cc_start: 0.8467 (p) cc_final: 0.8255 (p) REVERT: C 304 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7583 (mtm180) outliers start: 23 outliers final: 15 residues processed: 172 average time/residue: 1.0971 time to fit residues: 200.8081 Evaluate side-chains 178 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 244 ASN C 75 GLN C 220 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105856 restraints weight = 10989.340| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.45 r_work: 0.3343 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.218 Angle : 0.582 8.970 11373 Z= 0.315 Chirality : 0.043 0.186 1329 Planarity : 0.004 0.058 1430 Dihedral : 4.308 25.672 1166 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.94 % Allowed : 17.74 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.26), residues: 1074 helix: 3.07 (0.28), residues: 353 sheet: 1.00 (0.30), residues: 272 loop : -1.21 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 190 HIS 0.005 0.001 HIS E 35 PHE 0.025 0.002 PHE R 280 TYR 0.016 0.001 TYR B 163 ARG 0.015 0.000 ARG B 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3895.97 seconds wall clock time: 69 minutes 20.04 seconds (4160.04 seconds total)