Starting phenix.real_space_refine on Sat Aug 3 10:51:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrg_39542/08_2024/8yrg_39542.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrg_39542/08_2024/8yrg_39542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrg_39542/08_2024/8yrg_39542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrg_39542/08_2024/8yrg_39542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrg_39542/08_2024/8yrg_39542.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrg_39542/08_2024/8yrg_39542.cif" } resolution = 3.14 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= 0.001 sd= 0.021 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 1 5.49 5 S 51 5.16 5 C 5097 2.51 5 N 1368 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" 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 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 82": "NH1" <-> "NH2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7977 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 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 Chain: "R" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1723 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A1LZU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.64 Number of scatterers: 7977 At special positions: 0 Unit cell: (88, 115.28, 125.84, 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 51 16.00 P 1 15.00 O 1460 8.00 N 1368 7.00 C 5097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 95 through 102 removed outlier: 4.043A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP B 102 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.788A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.542A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.954A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 4.334A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.714A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 4.035A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 12 through 24 removed outlier: 4.199A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.878A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.000A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 55 Processing helix chain 'R' and resid 61 through 86 Proline residue: R 84 - end of helix Processing helix chain 'R' and resid 91 through 126 Proline residue: R 105 - end of helix removed outlier: 4.003A pdb=" N THR R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 153 removed outlier: 3.943A pdb=" N LEU R 151 " --> pdb=" O TRP R 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.771A pdb=" N ILE R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 228 removed outlier: 3.928A pdb=" N TYR R 215 " --> pdb=" O LEU R 211 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL R 216 " --> pdb=" O THR R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 242 removed outlier: 4.664A pdb=" N GLY R 233 " --> pdb=" O GLY R 229 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 274 removed outlier: 4.145A pdb=" N CYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Proline residue: R 269 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.644A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.551A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.635A 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: 6.885A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.551A 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 153 removed outlier: 3.740A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.634A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.508A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.828A 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: 6.345A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.025A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR E 94 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA E 92 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.685A 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 135 Processing sheet with id=AB3, first strand: chain 'E' and resid 144 through 147 Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.540A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 401 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: 2.56 Time building geometry restraints manager: 3.56 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: 2579 1.34 - 1.46: 1961 1.46 - 1.58: 3528 1.58 - 1.70: 1 1.70 - 1.82: 71 Bond restraints: 8140 Sorted by residual: bond pdb=" O2 A1LZU R 501 " pdb=" P1 A1LZU R 501 " ideal model delta sigma weight residual 1.740 1.617 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C13 A1LZU R 501 " pdb=" O2 A1LZU R 501 " ideal model delta sigma weight residual 1.364 1.403 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CG PRO E 224 " pdb=" CD PRO E 224 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.20e+00 bond pdb=" CG1 ILE C 273 " pdb=" CD1 ILE C 273 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 ... (remaining 8135 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 128 105.81 - 112.87: 4431 112.87 - 119.93: 2597 119.93 - 126.99: 3846 126.99 - 134.06: 89 Bond angle restraints: 11091 Sorted by residual: angle pdb=" N GLU B 25 " pdb=" CA GLU B 25 " pdb=" CB GLU B 25 " ideal model delta sigma weight residual 110.16 114.75 -4.59 1.48e+00 4.57e-01 9.61e+00 angle pdb=" C GLN E 113 " pdb=" N GLY E 114 " pdb=" CA GLY E 114 " ideal model delta sigma weight residual 121.58 119.14 2.44 8.60e-01 1.35e+00 8.05e+00 angle pdb=" N VAL R 101 " pdb=" CA VAL R 101 " pdb=" C VAL R 101 " ideal model delta sigma weight residual 113.00 109.41 3.59 1.30e+00 5.92e-01 7.64e+00 angle pdb=" CA LEU C 70 " pdb=" CB LEU C 70 " pdb=" CG LEU C 70 " ideal model delta sigma weight residual 116.30 125.92 -9.62 3.50e+00 8.16e-02 7.55e+00 angle pdb=" O1 A1LZU R 501 " pdb=" C13 A1LZU R 501 " pdb=" O2 A1LZU R 501 " ideal model delta sigma weight residual 106.35 113.87 -7.52 3.00e+00 1.11e-01 6.29e+00 ... (remaining 11086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4343 16.52 - 33.04: 340 33.04 - 49.56: 71 49.56 - 66.07: 6 66.07 - 82.59: 5 Dihedral angle restraints: 4765 sinusoidal: 1640 harmonic: 3125 Sorted by residual: dihedral pdb=" CA LEU R 156 " pdb=" C LEU R 156 " pdb=" N GLU R 157 " pdb=" CA GLU R 157 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU B 34 " pdb=" C LEU B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 949 0.049 - 0.097: 297 0.097 - 0.146: 56 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CG LEU B 245 " pdb=" CB LEU B 245 " pdb=" CD1 LEU B 245 " pdb=" CD2 LEU B 245 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE R 179 " pdb=" CA ILE R 179 " pdb=" CG1 ILE R 179 " pdb=" CG2 ILE R 179 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CG LEU E 79 " pdb=" CB LEU E 79 " pdb=" CD1 LEU E 79 " pdb=" CD2 LEU E 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1302 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO B 213 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 49 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 251 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C CYS R 251 " -0.030 2.00e-02 2.50e+03 pdb=" O CYS R 251 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS R 252 " 0.010 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 92 2.65 - 3.22: 7321 3.22 - 3.78: 11892 3.78 - 4.34: 16092 4.34 - 4.90: 27578 Nonbonded interactions: 62975 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O GLY R 229 " model vdw 2.093 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.101 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.147 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.192 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.212 3.040 ... (remaining 62970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.720 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.007 0.123 8140 Z= 0.456 Angle : 0.691 9.616 11091 Z= 0.370 Chirality : 0.046 0.243 1305 Planarity : 0.004 0.051 1399 Dihedral : 12.794 82.592 2741 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.87 (0.25), residues: 1061 helix: 0.68 (0.27), residues: 350 sheet: -0.72 (0.30), residues: 286 loop : -1.46 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 339 HIS 0.009 0.002 HIS C 225 PHE 0.024 0.002 PHE C 151 TYR 0.023 0.002 TYR R 106 ARG 0.011 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.783 Fit side-chains REVERT: B 9 ASP cc_start: 0.6826 (m-30) cc_final: 0.6526 (m-30) REVERT: B 95 LYS cc_start: 0.7406 (tppp) cc_final: 0.6586 (tppp) REVERT: C 118 ASP cc_start: 0.6887 (p0) cc_final: 0.6539 (p0) REVERT: C 155 ASN cc_start: 0.7411 (p0) cc_final: 0.7207 (p0) REVERT: C 204 CYS cc_start: 0.7084 (m) cc_final: 0.6754 (m) REVERT: C 277 SER cc_start: 0.8098 (t) cc_final: 0.7768 (p) REVERT: C 298 ASP cc_start: 0.7208 (t70) cc_final: 0.6938 (t70) REVERT: C 333 ASP cc_start: 0.7068 (p0) cc_final: 0.6761 (p0) REVERT: R 112 MET cc_start: 0.7789 (mmt) cc_final: 0.7220 (mmt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2204 time to fit residues: 57.7269 Evaluate side-chains 187 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8140 Z= 0.239 Angle : 0.594 9.720 11091 Z= 0.306 Chirality : 0.043 0.177 1305 Planarity : 0.004 0.050 1399 Dihedral : 4.657 24.221 1173 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.89 % Allowed : 10.70 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.28 (0.26), residues: 1061 helix: 1.26 (0.28), residues: 352 sheet: -0.21 (0.30), residues: 290 loop : -1.39 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.004 0.001 HIS C 225 PHE 0.015 0.002 PHE R 273 TYR 0.020 0.002 TYR R 106 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 214 time to evaluate : 0.889 Fit side-chains REVERT: B 9 ASP cc_start: 0.6730 (m-30) cc_final: 0.6393 (m-30) REVERT: B 17 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7493 (mtmm) REVERT: B 95 LYS cc_start: 0.7536 (tppp) cc_final: 0.6991 (tppp) REVERT: B 130 ASN cc_start: 0.8334 (m-40) cc_final: 0.8114 (m-40) REVERT: C 118 ASP cc_start: 0.6784 (p0) cc_final: 0.6419 (p0) REVERT: C 135 VAL cc_start: 0.8087 (t) cc_final: 0.7834 (m) REVERT: C 155 ASN cc_start: 0.7429 (p0) cc_final: 0.7149 (p0) REVERT: C 251 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7344 (mtt-85) REVERT: C 277 SER cc_start: 0.8113 (t) cc_final: 0.7776 (p) REVERT: C 298 ASP cc_start: 0.7352 (t70) cc_final: 0.6977 (t70) REVERT: C 333 ASP cc_start: 0.6956 (p0) cc_final: 0.6716 (p0) REVERT: R 223 LEU cc_start: 0.8030 (mp) cc_final: 0.7616 (mp) outliers start: 7 outliers final: 5 residues processed: 214 average time/residue: 0.2287 time to fit residues: 64.1332 Evaluate side-chains 217 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8140 Z= 0.330 Angle : 0.624 10.277 11091 Z= 0.317 Chirality : 0.044 0.194 1305 Planarity : 0.004 0.050 1399 Dihedral : 4.630 22.713 1173 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.68 % Allowed : 13.38 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.23 (0.26), residues: 1061 helix: 1.29 (0.28), residues: 352 sheet: -0.09 (0.30), residues: 293 loop : -1.43 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.005 0.001 HIS B 214 PHE 0.020 0.002 PHE R 273 TYR 0.022 0.002 TYR R 106 ARG 0.004 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 0.806 Fit side-chains REVERT: B 9 ASP cc_start: 0.6759 (m-30) cc_final: 0.6422 (m-30) REVERT: B 25 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5858 (mp0) REVERT: B 95 LYS cc_start: 0.7545 (tppp) cc_final: 0.7266 (tppp) REVERT: B 230 ASP cc_start: 0.6413 (m-30) cc_final: 0.6132 (m-30) REVERT: C 118 ASP cc_start: 0.6835 (p0) cc_final: 0.6461 (p0) REVERT: C 135 VAL cc_start: 0.8084 (t) cc_final: 0.7840 (m) REVERT: C 155 ASN cc_start: 0.7452 (p0) cc_final: 0.7181 (p0) REVERT: C 298 ASP cc_start: 0.7367 (t70) cc_final: 0.6980 (t70) REVERT: R 223 LEU cc_start: 0.8015 (mp) cc_final: 0.7601 (mp) outliers start: 21 outliers final: 18 residues processed: 213 average time/residue: 0.2192 time to fit residues: 61.8636 Evaluate side-chains 222 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 258 MET Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8140 Z= 0.236 Angle : 0.571 10.331 11091 Z= 0.291 Chirality : 0.042 0.211 1305 Planarity : 0.004 0.046 1399 Dihedral : 4.406 23.436 1173 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.68 % Allowed : 14.78 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.01 (0.26), residues: 1061 helix: 1.60 (0.28), residues: 352 sheet: -0.02 (0.30), residues: 292 loop : -1.40 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.025 0.002 PHE R 273 TYR 0.015 0.002 TYR E 178 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.6716 (m-30) cc_final: 0.6390 (m-30) REVERT: B 17 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7402 (mtmm) REVERT: B 230 ASP cc_start: 0.6411 (m-30) cc_final: 0.6123 (m-30) REVERT: C 118 ASP cc_start: 0.6754 (p0) cc_final: 0.6417 (p0) REVERT: C 135 VAL cc_start: 0.8064 (t) cc_final: 0.7852 (m) REVERT: C 155 ASN cc_start: 0.7458 (p0) cc_final: 0.7179 (p0) REVERT: C 298 ASP cc_start: 0.7374 (t70) cc_final: 0.7012 (t70) REVERT: C 333 ASP cc_start: 0.6827 (p0) cc_final: 0.6595 (p0) outliers start: 21 outliers final: 18 residues processed: 212 average time/residue: 0.2085 time to fit residues: 58.4842 Evaluate side-chains 218 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 258 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 42 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8140 Z= 0.161 Angle : 0.539 9.130 11091 Z= 0.273 Chirality : 0.041 0.227 1305 Planarity : 0.003 0.040 1399 Dihedral : 4.094 24.009 1173 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.18 % Allowed : 15.03 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.27), residues: 1061 helix: 1.95 (0.29), residues: 353 sheet: 0.13 (0.30), residues: 292 loop : -1.28 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.026 0.001 PHE R 273 TYR 0.013 0.001 TYR E 178 ARG 0.005 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7425 (mtmm) REVERT: C 155 ASN cc_start: 0.7437 (p0) cc_final: 0.7216 (p0) REVERT: C 165 THR cc_start: 0.7526 (m) cc_final: 0.7080 (p) REVERT: C 200 VAL cc_start: 0.8602 (m) cc_final: 0.8290 (p) REVERT: C 228 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6025 (m-30) REVERT: C 259 GLN cc_start: 0.7750 (tt0) cc_final: 0.7548 (tt0) REVERT: C 298 ASP cc_start: 0.7325 (t70) cc_final: 0.7007 (t70) REVERT: C 333 ASP cc_start: 0.6781 (p0) cc_final: 0.6561 (p0) REVERT: E 83 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6803 (mmt) REVERT: R 112 MET cc_start: 0.7768 (mmt) cc_final: 0.7151 (mmt) REVERT: R 122 LEU cc_start: 0.8487 (mm) cc_final: 0.8157 (mt) REVERT: R 129 TRP cc_start: 0.8120 (t60) cc_final: 0.7606 (t60) REVERT: R 223 LEU cc_start: 0.8022 (mp) cc_final: 0.7610 (mp) outliers start: 25 outliers final: 16 residues processed: 215 average time/residue: 0.2037 time to fit residues: 58.0864 Evaluate side-chains 222 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 MET Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8140 Z= 0.319 Angle : 0.619 10.193 11091 Z= 0.312 Chirality : 0.044 0.241 1305 Planarity : 0.004 0.043 1399 Dihedral : 4.405 24.994 1173 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.44 % Allowed : 15.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.11 (0.26), residues: 1061 helix: 1.72 (0.28), residues: 352 sheet: -0.03 (0.30), residues: 295 loop : -1.28 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.005 0.001 HIS E 35 PHE 0.025 0.002 PHE R 273 TYR 0.021 0.002 TYR E 178 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.6776 (m-30) cc_final: 0.6434 (m-30) REVERT: B 17 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7454 (mtmm) REVERT: B 230 ASP cc_start: 0.6450 (m-30) cc_final: 0.6153 (m-30) REVERT: C 118 ASP cc_start: 0.6717 (p0) cc_final: 0.6334 (p0) REVERT: C 155 ASN cc_start: 0.7453 (p0) cc_final: 0.7200 (p0) REVERT: C 200 VAL cc_start: 0.8594 (m) cc_final: 0.8240 (p) REVERT: C 259 GLN cc_start: 0.7934 (tt0) cc_final: 0.7699 (tt0) REVERT: C 298 ASP cc_start: 0.7351 (t70) cc_final: 0.7001 (t70) REVERT: C 333 ASP cc_start: 0.6887 (p0) cc_final: 0.6661 (p0) REVERT: E 83 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6761 (mmt) REVERT: R 223 LEU cc_start: 0.8033 (mp) cc_final: 0.7613 (mp) outliers start: 27 outliers final: 21 residues processed: 221 average time/residue: 0.2083 time to fit residues: 61.0343 Evaluate side-chains 227 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 MET Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.0050 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8140 Z= 0.161 Angle : 0.557 10.508 11091 Z= 0.278 Chirality : 0.041 0.259 1305 Planarity : 0.003 0.038 1399 Dihedral : 4.043 26.241 1173 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.06 % Allowed : 17.32 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.43 (0.27), residues: 1061 helix: 2.09 (0.29), residues: 353 sheet: 0.13 (0.30), residues: 294 loop : -1.20 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE R 273 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7422 (mtmm) REVERT: C 155 ASN cc_start: 0.7440 (p0) cc_final: 0.7186 (p0) REVERT: C 200 VAL cc_start: 0.8574 (m) cc_final: 0.8246 (p) REVERT: C 228 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.6017 (m-30) REVERT: C 280 LYS cc_start: 0.7771 (tttp) cc_final: 0.7542 (tttp) REVERT: C 298 ASP cc_start: 0.7287 (t70) cc_final: 0.6974 (t70) REVERT: C 333 ASP cc_start: 0.6774 (p0) cc_final: 0.6568 (p0) REVERT: R 112 MET cc_start: 0.7732 (mmt) cc_final: 0.7139 (mmt) REVERT: R 122 LEU cc_start: 0.8490 (mm) cc_final: 0.8156 (mt) REVERT: R 129 TRP cc_start: 0.8101 (t60) cc_final: 0.7580 (t60) REVERT: R 223 LEU cc_start: 0.8025 (mp) cc_final: 0.7617 (mp) outliers start: 24 outliers final: 18 residues processed: 217 average time/residue: 0.2063 time to fit residues: 59.2009 Evaluate side-chains 225 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 80 optimal weight: 0.0270 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8140 Z= 0.154 Angle : 0.553 11.009 11091 Z= 0.275 Chirality : 0.041 0.255 1305 Planarity : 0.003 0.036 1399 Dihedral : 3.918 25.827 1173 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.55 % Allowed : 18.60 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.60 (0.27), residues: 1061 helix: 2.20 (0.29), residues: 353 sheet: 0.24 (0.31), residues: 294 loop : -1.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE R 273 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7407 (mtmm) REVERT: B 21 LYS cc_start: 0.7498 (ttpp) cc_final: 0.7244 (ttpp) REVERT: C 155 ASN cc_start: 0.7445 (p0) cc_final: 0.7191 (p0) REVERT: C 200 VAL cc_start: 0.8569 (m) cc_final: 0.8202 (p) REVERT: C 228 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6042 (m-30) REVERT: C 234 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: C 280 LYS cc_start: 0.7771 (tttp) cc_final: 0.7557 (tttp) REVERT: C 298 ASP cc_start: 0.7246 (t70) cc_final: 0.7022 (t70) REVERT: E 83 MET cc_start: 0.7478 (mtm) cc_final: 0.7106 (mtt) REVERT: R 112 MET cc_start: 0.7778 (mmt) cc_final: 0.7213 (mmt) REVERT: R 122 LEU cc_start: 0.8482 (mm) cc_final: 0.8145 (mt) REVERT: R 129 TRP cc_start: 0.8091 (t60) cc_final: 0.7569 (t60) REVERT: R 223 LEU cc_start: 0.8041 (mp) cc_final: 0.7639 (mp) outliers start: 20 outliers final: 17 residues processed: 217 average time/residue: 0.2167 time to fit residues: 62.2080 Evaluate side-chains 232 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8140 Z= 0.178 Angle : 0.569 10.580 11091 Z= 0.282 Chirality : 0.041 0.258 1305 Planarity : 0.003 0.037 1399 Dihedral : 3.938 25.348 1173 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.93 % Allowed : 18.47 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.62 (0.27), residues: 1061 helix: 2.21 (0.29), residues: 353 sheet: 0.25 (0.31), residues: 294 loop : -1.07 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE R 273 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7413 (mtmm) REVERT: B 21 LYS cc_start: 0.7495 (ttpp) cc_final: 0.7243 (ttpp) REVERT: C 118 ASP cc_start: 0.6547 (p0) cc_final: 0.6226 (p0) REVERT: C 155 ASN cc_start: 0.7461 (p0) cc_final: 0.7202 (p0) REVERT: C 200 VAL cc_start: 0.8569 (m) cc_final: 0.8218 (p) REVERT: C 228 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6016 (m-30) REVERT: C 234 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: C 280 LYS cc_start: 0.7781 (tttp) cc_final: 0.7563 (tttp) REVERT: C 298 ASP cc_start: 0.7245 (t70) cc_final: 0.7011 (t70) REVERT: E 83 MET cc_start: 0.7337 (mtm) cc_final: 0.6966 (mtt) REVERT: R 95 ARG cc_start: 0.6891 (mtt180) cc_final: 0.6679 (mtt90) REVERT: R 112 MET cc_start: 0.7764 (mmt) cc_final: 0.7158 (mmt) REVERT: R 122 LEU cc_start: 0.8480 (mm) cc_final: 0.8146 (mt) REVERT: R 129 TRP cc_start: 0.8102 (t60) cc_final: 0.7566 (t60) REVERT: R 223 LEU cc_start: 0.8026 (mp) cc_final: 0.7633 (mp) outliers start: 23 outliers final: 21 residues processed: 210 average time/residue: 0.2113 time to fit residues: 58.3940 Evaluate side-chains 223 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 MET Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8140 Z= 0.153 Angle : 0.554 10.992 11091 Z= 0.274 Chirality : 0.041 0.258 1305 Planarity : 0.003 0.036 1399 Dihedral : 3.810 24.591 1173 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.68 % Allowed : 19.36 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.75 (0.27), residues: 1061 helix: 2.29 (0.29), residues: 358 sheet: 0.27 (0.31), residues: 295 loop : -0.95 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE R 273 TYR 0.013 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7416 (mtmm) REVERT: B 21 LYS cc_start: 0.7499 (ttpp) cc_final: 0.7248 (ttpp) REVERT: C 155 ASN cc_start: 0.7476 (p0) cc_final: 0.7203 (p0) REVERT: C 200 VAL cc_start: 0.8575 (m) cc_final: 0.8231 (p) REVERT: C 228 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.6027 (m-30) REVERT: C 234 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: C 251 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7196 (mtt180) REVERT: C 280 LYS cc_start: 0.7765 (tttp) cc_final: 0.7558 (tttp) REVERT: C 298 ASP cc_start: 0.7219 (t70) cc_final: 0.6991 (t70) REVERT: E 83 MET cc_start: 0.7364 (mtm) cc_final: 0.7011 (mtt) REVERT: R 95 ARG cc_start: 0.6865 (mtt180) cc_final: 0.6664 (mtt90) REVERT: R 112 MET cc_start: 0.7754 (mmt) cc_final: 0.7198 (mmt) REVERT: R 122 LEU cc_start: 0.8487 (mm) cc_final: 0.8149 (mt) REVERT: R 129 TRP cc_start: 0.8081 (t60) cc_final: 0.7526 (t60) REVERT: R 213 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6967 (ttt180) outliers start: 21 outliers final: 16 residues processed: 209 average time/residue: 0.2010 time to fit residues: 56.0790 Evaluate side-chains 219 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125604 restraints weight = 11862.345| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.32 r_work: 0.3439 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8140 Z= 0.190 Angle : 0.574 10.938 11091 Z= 0.284 Chirality : 0.042 0.256 1305 Planarity : 0.004 0.038 1399 Dihedral : 3.900 25.027 1173 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.29 % Allowed : 20.51 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.71 (0.27), residues: 1061 helix: 2.32 (0.28), residues: 353 sheet: 0.27 (0.31), residues: 288 loop : -1.00 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 158 HIS 0.004 0.001 HIS E 35 PHE 0.027 0.001 PHE R 273 TYR 0.016 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2198.48 seconds wall clock time: 39 minutes 13.33 seconds (2353.33 seconds total)