Starting phenix.real_space_refine on Fri Mar 14 00:59:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ic0_35351/03_2025/8ic0_35351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ic0_35351/03_2025/8ic0_35351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ic0_35351/03_2025/8ic0_35351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ic0_35351/03_2025/8ic0_35351.map" model { file = "/net/cci-nas-00/data/ceres_data/8ic0_35351/03_2025/8ic0_35351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ic0_35351/03_2025/8ic0_35351.cif" } resolution = 3.41 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= 0.005 sd= 0.048 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 71 5.16 5 C 6100 2.51 5 N 1638 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9553 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2420 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 564 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Time building chain proxies: 5.75, per 1000 atoms: 0.60 Number of scatterers: 9553 At special positions: 0 Unit cell: (91.216, 122.337, 149.165, 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 71 16.00 O 1744 8.00 N 1638 7.00 C 6100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 34 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 50 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 35 through 68 removed outlier: 3.521A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 102 removed outlier: 3.980A pdb=" N VAL A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.858A pdb=" N SER A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 140 removed outlier: 3.585A pdb=" N LYS A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.582A pdb=" N ASN A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.830A pdb=" N PHE A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.892A pdb=" N VAL A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.760A pdb=" N HIS A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 3.594A pdb=" N PHE A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 270 removed outlier: 3.692A pdb=" N ILE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.645A pdb=" N THR A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.579A pdb=" N ASN A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 4.476A pdb=" N ILE A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.674A pdb=" N HIS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 removed outlier: 4.600A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.676A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.273A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.957A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.522A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.784A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 352 removed outlier: 4.236A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 4.070A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.883A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.304A 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 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.526A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.842A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.709A 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: 3.703A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.895A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.517A pdb=" N GLN F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 61 " --> pdb=" O TRP F 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 186 removed outlier: 3.906A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.163A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.957A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.378A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 149 through 153 removed outlier: 6.613A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.724A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.688A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.446A 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: 3.507A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.365A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.622A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.528A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 178 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 28 removed outlier: 4.475A pdb=" N GLU F 24 " --> pdb=" O LYS F 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS F 42 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 38 " --> pdb=" O ILE F 28 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1014 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: 2.50 Time building geometry restraints manager: 2.81 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: 3081 1.34 - 1.46: 2281 1.46 - 1.58: 4289 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9752 Sorted by residual: bond pdb=" CB PRO A 180 " pdb=" CG PRO A 180 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.46e+00 bond pdb=" CA PHE A 174 " pdb=" CB PHE A 174 " ideal model delta sigma weight residual 1.528 1.569 -0.040 2.61e-02 1.47e+03 2.38e+00 bond pdb=" C ASP C 333 " pdb=" N SER C 334 " ideal model delta sigma weight residual 1.332 1.312 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.35e+00 bond pdb=" CA ILE A 139 " pdb=" CB ILE A 139 " ideal model delta sigma weight residual 1.545 1.535 0.010 9.10e-03 1.21e+04 1.32e+00 ... (remaining 9747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 12835 1.35 - 2.70: 285 2.70 - 4.06: 57 4.06 - 5.41: 26 5.41 - 6.76: 6 Bond angle restraints: 13209 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 107.78 5.93 9.50e-01 1.11e+00 3.89e+01 angle pdb=" N ILE C 33 " pdb=" CA ILE C 33 " pdb=" C ILE C 33 " ideal model delta sigma weight residual 113.42 108.77 4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" N VAL A 272 " pdb=" CA VAL A 272 " pdb=" C VAL A 272 " ideal model delta sigma weight residual 111.56 108.59 2.97 8.60e-01 1.35e+00 1.19e+01 angle pdb=" C ASP C 118 " pdb=" N ASN C 119 " pdb=" CA ASN C 119 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 115.75 5.79 1.91e+00 2.74e-01 9.19e+00 ... (remaining 13204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5225 17.54 - 35.08: 479 35.08 - 52.62: 87 52.62 - 70.16: 11 70.16 - 87.69: 7 Dihedral angle restraints: 5809 sinusoidal: 2247 harmonic: 3562 Sorted by residual: dihedral pdb=" CA TYR E 178 " pdb=" C TYR E 178 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " ideal model delta harmonic sigma weight residual -180.00 -144.01 -35.99 0 5.00e+00 4.00e-02 5.18e+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 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -131.34 45.34 1 1.00e+01 1.00e-02 2.85e+01 ... (remaining 5806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 960 0.032 - 0.064: 392 0.064 - 0.096: 89 0.096 - 0.127: 66 0.127 - 0.159: 4 Chirality restraints: 1511 Sorted by residual: chirality pdb=" CA ASN C 119 " pdb=" N ASN C 119 " pdb=" C ASN C 119 " pdb=" CB ASN C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA TRP C 332 " pdb=" N TRP C 332 " pdb=" C TRP C 332 " pdb=" CB TRP C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1508 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 179 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 180 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " 0.018 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP C 332 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 194 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.027 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 9590 3.26 - 3.81: 14494 3.81 - 4.35: 18741 4.35 - 4.90: 31644 Nonbonded interactions: 74757 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.163 3.040 nonbonded pdb=" OE1 GLN E 130 " pdb=" OG1 THR E 231 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 192 " pdb=" OG1 THR E 203 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR E 101 " pdb=" NE2 HIS E 220 " model vdw 2.292 3.120 nonbonded pdb=" OH TYR C 289 " pdb=" NE1 TRP C 297 " model vdw 2.300 3.120 ... (remaining 74752 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: 0.540 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.330 Find NCS groups from input model: 0.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.078 9752 Z= 0.199 Angle : 0.550 6.760 13209 Z= 0.296 Chirality : 0.041 0.159 1511 Planarity : 0.004 0.104 1665 Dihedral : 13.845 87.694 3491 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.57 (0.24), residues: 1212 helix: 0.04 (0.27), residues: 373 sheet: -1.48 (0.34), residues: 258 loop : -1.49 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 332 HIS 0.006 0.001 HIS B 188 PHE 0.020 0.001 PHE A 174 TYR 0.025 0.001 TYR E 178 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.6706 (tpp) cc_final: 0.6252 (ttm) REVERT: C 61 MET cc_start: 0.7823 (ppp) cc_final: 0.7478 (ppp) REVERT: E 13 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7871 (mm110) REVERT: E 77 ASN cc_start: 0.7464 (t0) cc_final: 0.7260 (t0) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2054 time to fit residues: 40.1091 Evaluate side-chains 110 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS B 331 ASN C 220 GLN C 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.195403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126531 restraints weight = 11242.880| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.27 r_work: 0.3334 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9752 Z= 0.307 Angle : 0.625 7.221 13209 Z= 0.326 Chirality : 0.044 0.139 1511 Planarity : 0.005 0.064 1665 Dihedral : 4.523 33.832 1327 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.88 % Allowed : 10.03 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.19 (0.24), residues: 1212 helix: 0.63 (0.26), residues: 380 sheet: -1.44 (0.33), residues: 261 loop : -1.40 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 332 HIS 0.006 0.001 HIS B 188 PHE 0.019 0.002 PHE A 174 TYR 0.030 0.002 TYR E 178 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.7380 (mtm) cc_final: 0.6825 (mtm) REVERT: B 53 MET cc_start: 0.6442 (tpp) cc_final: 0.6240 (ttm) REVERT: C 61 MET cc_start: 0.8539 (ppp) cc_final: 0.8254 (ppp) REVERT: D 42 GLU cc_start: 0.8368 (pp20) cc_final: 0.7928 (mm-30) outliers start: 9 outliers final: 6 residues processed: 128 average time/residue: 0.2233 time to fit residues: 40.2830 Evaluate side-chains 119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 104 optimal weight: 30.0000 chunk 110 optimal weight: 0.0050 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.198312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131284 restraints weight = 11339.758| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.36 r_work: 0.3345 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9752 Z= 0.171 Angle : 0.542 6.736 13209 Z= 0.279 Chirality : 0.041 0.136 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.269 33.427 1327 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.88 % Allowed : 13.34 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.01 (0.24), residues: 1212 helix: 0.97 (0.27), residues: 380 sheet: -1.48 (0.33), residues: 253 loop : -1.37 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 174 TYR 0.026 0.001 TYR E 178 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8901 (mp10) cc_final: 0.8643 (mp10) REVERT: C 61 MET cc_start: 0.8491 (ppp) cc_final: 0.8273 (ppp) REVERT: D 42 GLU cc_start: 0.8305 (pp20) cc_final: 0.7915 (mm-30) REVERT: E 18 ARG cc_start: 0.6034 (mtp85) cc_final: 0.5558 (mtp180) REVERT: E 77 ASN cc_start: 0.6603 (t0) cc_final: 0.6157 (t0) outliers start: 9 outliers final: 5 residues processed: 131 average time/residue: 0.2190 time to fit residues: 40.7276 Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 70.0000 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.194795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124957 restraints weight = 11312.866| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.91 r_work: 0.3340 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9752 Z= 0.297 Angle : 0.591 7.961 13209 Z= 0.303 Chirality : 0.043 0.137 1511 Planarity : 0.004 0.054 1665 Dihedral : 4.422 33.337 1327 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.85 % Allowed : 14.90 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.00 (0.24), residues: 1212 helix: 0.97 (0.27), residues: 379 sheet: -1.42 (0.32), residues: 264 loop : -1.38 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 211 HIS 0.014 0.001 HIS C 266 PHE 0.015 0.001 PHE E 27 TYR 0.027 0.002 TYR E 178 ARG 0.005 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.997 Fit side-chains REVERT: C 61 MET cc_start: 0.8617 (ppp) cc_final: 0.8263 (ppp) REVERT: C 220 GLN cc_start: 0.8552 (mt0) cc_final: 0.8079 (mt0) REVERT: C 234 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.6549 (t80) REVERT: D 42 GLU cc_start: 0.8318 (pp20) cc_final: 0.7926 (mm-30) REVERT: E 77 ASN cc_start: 0.6854 (t0) cc_final: 0.6290 (t0) REVERT: E 160 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7348 (t) outliers start: 19 outliers final: 9 residues processed: 122 average time/residue: 0.1953 time to fit residues: 34.5538 Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.194301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129618 restraints weight = 11469.815| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.48 r_work: 0.3311 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9752 Z= 0.153 Angle : 0.527 7.516 13209 Z= 0.268 Chirality : 0.040 0.135 1511 Planarity : 0.003 0.051 1665 Dihedral : 4.130 32.256 1327 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.85 % Allowed : 15.87 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.80 (0.24), residues: 1212 helix: 1.17 (0.27), residues: 379 sheet: -1.29 (0.32), residues: 279 loop : -1.29 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE E 29 TYR 0.023 0.001 TYR E 178 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.951 Fit side-chains REVERT: A 165 MET cc_start: 0.5226 (mmt) cc_final: 0.3872 (mtp) REVERT: C 61 MET cc_start: 0.8437 (ppp) cc_final: 0.8212 (ppp) REVERT: C 191 SER cc_start: 0.8117 (t) cc_final: 0.7870 (p) REVERT: C 220 GLN cc_start: 0.8598 (mt0) cc_final: 0.8159 (mt0) REVERT: C 234 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.6799 (t80) REVERT: D 42 GLU cc_start: 0.8318 (pp20) cc_final: 0.8012 (mm-30) REVERT: E 18 ARG cc_start: 0.5980 (mtp85) cc_final: 0.5451 (mtp180) REVERT: E 160 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7480 (t) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.2311 time to fit residues: 44.2323 Evaluate side-chains 126 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 40.0000 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN B 333 GLN C 183 HIS ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.187346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120884 restraints weight = 11717.713| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.51 r_work: 0.3208 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9752 Z= 0.449 Angle : 0.678 8.366 13209 Z= 0.348 Chirality : 0.046 0.168 1511 Planarity : 0.005 0.074 1665 Dihedral : 4.720 33.358 1327 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.21 % Allowed : 16.85 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.17 (0.24), residues: 1212 helix: 0.87 (0.26), residues: 381 sheet: -1.67 (0.31), residues: 270 loop : -1.43 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 211 HIS 0.008 0.002 HIS B 188 PHE 0.021 0.002 PHE E 27 TYR 0.029 0.002 TYR E 178 ARG 0.004 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 1.009 Fit side-chains REVERT: A 241 MET cc_start: 0.7755 (ttt) cc_final: 0.7445 (ttp) REVERT: C 117 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8005 (tp) REVERT: C 188 MET cc_start: 0.7418 (mtt) cc_final: 0.6679 (mtt) REVERT: C 220 GLN cc_start: 0.8719 (mt0) cc_final: 0.8422 (mt0) REVERT: C 234 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.6535 (t80) REVERT: D 42 GLU cc_start: 0.8408 (pp20) cc_final: 0.7970 (mm-30) REVERT: E 160 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7641 (t) REVERT: E 225 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7881 (pt) outliers start: 33 outliers final: 16 residues processed: 136 average time/residue: 0.2627 time to fit residues: 53.1018 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.190270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123178 restraints weight = 11632.559| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.67 r_work: 0.3246 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9752 Z= 0.245 Angle : 0.578 8.481 13209 Z= 0.296 Chirality : 0.042 0.159 1511 Planarity : 0.003 0.053 1665 Dihedral : 4.474 32.884 1327 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.53 % Allowed : 18.11 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.11 (0.24), residues: 1212 helix: 0.99 (0.27), residues: 383 sheet: -1.64 (0.31), residues: 275 loop : -1.45 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS B 188 PHE 0.014 0.001 PHE E 27 TYR 0.022 0.001 TYR E 178 ARG 0.004 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.047 Fit side-chains REVERT: A 165 MET cc_start: 0.5105 (mmt) cc_final: 0.3792 (mtp) REVERT: A 241 MET cc_start: 0.7768 (ttt) cc_final: 0.7454 (ttp) REVERT: C 191 SER cc_start: 0.8018 (t) cc_final: 0.7776 (p) REVERT: C 220 GLN cc_start: 0.8718 (mt0) cc_final: 0.8323 (mt0) REVERT: C 234 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.6633 (t80) REVERT: D 42 GLU cc_start: 0.8401 (pp20) cc_final: 0.7943 (mm-30) REVERT: E 160 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7552 (t) REVERT: E 221 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8177 (mt) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.1966 time to fit residues: 37.0550 Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 75 GLN C 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.193358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127869 restraints weight = 11637.240| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.58 r_work: 0.3301 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9752 Z= 0.150 Angle : 0.548 8.698 13209 Z= 0.277 Chirality : 0.040 0.153 1511 Planarity : 0.003 0.052 1665 Dihedral : 4.194 32.503 1327 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.85 % Allowed : 18.60 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.95 (0.24), residues: 1212 helix: 1.22 (0.27), residues: 383 sheet: -1.45 (0.31), residues: 273 loop : -1.49 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE E 29 TYR 0.021 0.001 TYR E 178 ARG 0.003 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.066 Fit side-chains REVERT: A 85 ASP cc_start: 0.7548 (m-30) cc_final: 0.7294 (t0) REVERT: A 165 MET cc_start: 0.5051 (mmt) cc_final: 0.3724 (mtp) REVERT: C 188 MET cc_start: 0.7184 (mtt) cc_final: 0.6957 (mtt) REVERT: C 191 SER cc_start: 0.8035 (t) cc_final: 0.7793 (p) REVERT: C 220 GLN cc_start: 0.8685 (mt0) cc_final: 0.8257 (mt0) REVERT: C 234 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.6715 (t80) REVERT: D 42 GLU cc_start: 0.8323 (pp20) cc_final: 0.7860 (mm-30) outliers start: 19 outliers final: 15 residues processed: 132 average time/residue: 0.2099 time to fit residues: 40.4329 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 57 optimal weight: 0.0770 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 4.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 75 GLN C 183 HIS ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123267 restraints weight = 12092.684| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.14 r_work: 0.3300 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 9752 Z= 0.583 Angle : 0.760 8.480 13209 Z= 0.391 Chirality : 0.049 0.215 1511 Planarity : 0.005 0.079 1665 Dihedral : 4.949 32.818 1327 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.73 % Allowed : 18.50 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.49 (0.24), residues: 1212 helix: 0.73 (0.26), residues: 383 sheet: -1.91 (0.31), residues: 262 loop : -1.70 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 211 HIS 0.011 0.002 HIS B 188 PHE 0.028 0.002 PHE A 121 TYR 0.032 0.002 TYR E 178 ARG 0.005 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.072 Fit side-chains REVERT: A 241 MET cc_start: 0.7947 (ttt) cc_final: 0.7666 (ttp) REVERT: A 271 GLN cc_start: 0.8667 (mp10) cc_final: 0.8376 (mp10) REVERT: C 234 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.6827 (t80) REVERT: D 42 GLU cc_start: 0.8464 (pp20) cc_final: 0.8061 (mm-30) outliers start: 28 outliers final: 18 residues processed: 130 average time/residue: 0.1983 time to fit residues: 37.4613 Evaluate side-chains 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 118 optimal weight: 30.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 183 HIS C 220 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.190746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120128 restraints weight = 11587.616| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.12 r_work: 0.3290 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9752 Z= 0.189 Angle : 0.589 9.296 13209 Z= 0.296 Chirality : 0.041 0.148 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.444 32.733 1327 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.75 % Allowed : 19.38 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.19 (0.24), residues: 1212 helix: 1.05 (0.27), residues: 383 sheet: -1.76 (0.31), residues: 269 loop : -1.57 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.005 0.001 HIS B 188 PHE 0.013 0.001 PHE E 29 TYR 0.021 0.001 TYR E 178 ARG 0.004 0.000 ARG D 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.033 Fit side-chains REVERT: A 165 MET cc_start: 0.4968 (mmt) cc_final: 0.3662 (mtp) REVERT: A 241 MET cc_start: 0.7738 (ttt) cc_final: 0.7409 (ttp) REVERT: A 271 GLN cc_start: 0.8752 (mp10) cc_final: 0.8534 (mp10) REVERT: C 146 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7618 (tt) REVERT: C 188 MET cc_start: 0.7312 (mtt) cc_final: 0.6618 (mtt) REVERT: C 191 SER cc_start: 0.7963 (t) cc_final: 0.7701 (p) REVERT: C 234 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.6660 (t80) REVERT: C 239 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7597 (t0) REVERT: D 42 GLU cc_start: 0.8373 (pp20) cc_final: 0.7835 (mm-30) REVERT: E 93 MET cc_start: 0.7718 (ptt) cc_final: 0.7506 (ppp) outliers start: 18 outliers final: 14 residues processed: 123 average time/residue: 0.2092 time to fit residues: 37.5064 Evaluate side-chains 127 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 220 GLN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.190028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124065 restraints weight = 11545.025| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.63 r_work: 0.3231 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9752 Z= 0.230 Angle : 0.602 9.643 13209 Z= 0.302 Chirality : 0.042 0.163 1511 Planarity : 0.004 0.053 1665 Dihedral : 4.434 33.104 1327 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.24 % Allowed : 19.28 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.17 (0.24), residues: 1212 helix: 1.12 (0.27), residues: 383 sheet: -1.76 (0.31), residues: 259 loop : -1.61 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.006 0.001 HIS B 188 PHE 0.012 0.001 PHE A 121 TYR 0.025 0.001 TYR E 178 ARG 0.004 0.000 ARG D 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.80 seconds wall clock time: 89 minutes 34.96 seconds (5374.96 seconds total)