Starting phenix.real_space_refine on Mon Mar 11 14:26:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0339/03_2024/6n4b_0339_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0339/03_2024/6n4b_0339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0339/03_2024/6n4b_0339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0339/03_2024/6n4b_0339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0339/03_2024/6n4b_0339_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0339/03_2024/6n4b_0339_neut_updated.pdb" } resolution = 3.0 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= 0.030 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 S 58 5.16 5 C 5423 2.51 5 N 1457 2.21 5 O 1514 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 208": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "R ARG 186": "NH1" <-> "NH2" Residue "R ARG 230": "NH1" <-> "NH2" Residue "R ARG 311": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 400": "NH1" <-> "NH2" Residue "R ARG 405": "NH1" <-> "NH2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 206": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8453 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" 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: "R" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1988 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'CLR': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.15, per 1000 atoms: 0.61 Number of scatterers: 8453 At special positions: 0 Unit cell: (109.22, 122.98, 109.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 1 9.00 O 1514 8.00 N 1457 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 31.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.718A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.798A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.244A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.577A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.987A pdb=" N VAL A 332 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 340 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 344 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 348 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 350 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.550A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.622A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'R' and resid 113 through 142 removed outlier: 4.519A pdb=" N VAL R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER R 123 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 149 No H-bonds generated for 'chain 'R' and resid 146 through 149' Processing helix chain 'R' and resid 151 through 177 removed outlier: 3.937A pdb=" N PHE R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 162 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 190 removed outlier: 4.288A pdb=" N LEU R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 186 through 190' Processing helix chain 'R' and resid 194 through 219 removed outlier: 3.622A pdb=" N ILE R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 227 removed outlier: 4.523A pdb=" N LYS R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 253 removed outlier: 3.568A pdb=" N LEU R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 273 through 276 No H-bonds generated for 'chain 'R' and resid 273 through 276' Processing helix chain 'R' and resid 279 through 310 removed outlier: 3.580A pdb=" N ILE R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 357 removed outlier: 3.842A pdb=" N ALA R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS R 343 " --> pdb=" O ILE R 339 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE R 353 " --> pdb=" O LEU R 349 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 362 No H-bonds generated for 'chain 'R' and resid 359 through 362' Processing helix chain 'R' and resid 375 through 398 removed outlier: 3.708A pdb=" N ALA R 380 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE R 381 " --> pdb=" O THR R 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU R 387 " --> pdb=" O SER R 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU R 388 " --> pdb=" O MET R 384 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 402 through 409 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.946A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.918A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.568A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.090A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.765A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.601A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.888A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.660A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.708A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'S' and resid 213 through 219 removed outlier: 3.900A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 819 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: 2.34 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 1206 1.24 - 1.39: 2297 1.39 - 1.53: 4598 1.53 - 1.67: 451 1.67 - 1.81: 84 Bond restraints: 8636 Sorted by residual: bond pdb=" CAT KCA R 501 " pdb=" FAU KCA R 501 " ideal model delta sigma weight residual 1.342 1.101 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" CAB KCA R 501 " pdb=" CAM KCA R 501 " ideal model delta sigma weight residual 1.476 1.351 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CA TRP B 339 " pdb=" C TRP B 339 " ideal model delta sigma weight residual 1.523 1.457 0.067 1.18e-02 7.18e+03 3.19e+01 bond pdb=" CAP KCA R 501 " pdb=" CAQ KCA R 501 " ideal model delta sigma weight residual 1.507 1.395 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.19e-02 7.06e+03 2.07e+01 ... (remaining 8631 not shown) Histogram of bond angle deviations from ideal: 97.43 - 105.71: 182 105.71 - 113.99: 4945 113.99 - 122.27: 5238 122.27 - 130.55: 1331 130.55 - 138.82: 52 Bond angle restraints: 11748 Sorted by residual: angle pdb=" N PHE R 177 " pdb=" CA PHE R 177 " pdb=" C PHE R 177 " ideal model delta sigma weight residual 111.14 123.07 -11.93 1.08e+00 8.57e-01 1.22e+02 angle pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 120.60 137.91 -17.31 2.20e+00 2.07e-01 6.19e+01 angle pdb=" N TYR R 397 " pdb=" CA TYR R 397 " pdb=" C TYR R 397 " ideal model delta sigma weight residual 111.36 119.69 -8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N LEU R 193 " pdb=" CA LEU R 193 " pdb=" C LEU R 193 " ideal model delta sigma weight residual 114.39 103.36 11.03 1.45e+00 4.76e-01 5.78e+01 angle pdb=" N LEU S 225 " pdb=" CA LEU S 225 " pdb=" C LEU S 225 " ideal model delta sigma weight residual 111.17 121.84 -10.67 1.41e+00 5.03e-01 5.73e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4939 17.03 - 34.07: 177 34.07 - 51.10: 34 51.10 - 68.14: 9 68.14 - 85.17: 2 Dihedral angle restraints: 5161 sinusoidal: 1911 harmonic: 3250 Sorted by residual: dihedral pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " ideal model delta harmonic sigma weight residual 122.80 143.79 -20.99 0 2.50e+00 1.60e-01 7.05e+01 dihedral pdb=" C TYR S 178 " pdb=" N TYR S 178 " pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " ideal model delta harmonic sigma weight residual -122.60 -142.31 19.71 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" C TRP R 241 " pdb=" N TRP R 241 " pdb=" CA TRP R 241 " pdb=" CB TRP R 241 " ideal model delta harmonic sigma weight residual -122.60 -139.20 16.60 0 2.50e+00 1.60e-01 4.41e+01 ... (remaining 5158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 1319 0.187 - 0.374: 42 0.374 - 0.561: 7 0.561 - 0.749: 1 0.749 - 0.936: 1 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CA TRP R 241 " pdb=" N TRP R 241 " pdb=" C TRP R 241 " pdb=" CB TRP R 241 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA LEU S 225 " pdb=" N LEU S 225 " pdb=" C LEU S 225 " pdb=" CB LEU S 225 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.56e+00 ... (remaining 1367 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " -0.032 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP S 111 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 394 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C PRO R 394 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO R 394 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE R 395 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 256 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" CG ASN A 256 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 256 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 256 " 0.023 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 52 2.46 - 3.07: 5970 3.07 - 3.68: 11478 3.68 - 4.29: 16720 4.29 - 4.90: 28836 Nonbonded interactions: 63056 Sorted by model distance: nonbonded pdb=" CE MET R 371 " pdb=" CB ILE R 375 " model vdw 1.855 3.890 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 1.962 2.440 nonbonded pdb=" O ASP B 38 " pdb=" OD1 ASP B 38 " model vdw 1.981 3.040 nonbonded pdb=" O HIS S 220 " pdb=" ND1 HIS S 220 " model vdw 2.011 2.520 nonbonded pdb=" CD1 ILE S 126 " pdb=" OE2 GLU S 222 " model vdw 2.077 3.460 ... (remaining 63051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.330 Find NCS groups from input model: 0.260 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.011 0.241 8636 Z= 0.736 Angle : 1.400 17.310 11748 Z= 0.876 Chirality : 0.091 0.936 1370 Planarity : 0.008 0.075 1463 Dihedral : 9.763 85.169 3058 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.84 % Allowed : 2.88 % Favored : 96.28 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.23), residues: 1101 helix: -1.09 (0.27), residues: 320 sheet: -1.55 (0.30), residues: 253 loop : -1.65 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP S 111 HIS 0.011 0.003 HIS R 143 PHE 0.030 0.004 PHE A 196 TYR 0.049 0.005 TYR A 287 ARG 0.010 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 0.974 Fit side-chains REVERT: A 14 GLU cc_start: 0.7919 (tt0) cc_final: 0.7571 (tt0) REVERT: B 13 GLN cc_start: 0.7174 (mt0) cc_final: 0.6929 (tt0) REVERT: C 18 GLN cc_start: 0.7284 (tp-100) cc_final: 0.7065 (tp-100) REVERT: R 186 ARG cc_start: 0.6786 (mtm180) cc_final: 0.5387 (ttt180) REVERT: R 347 LEU cc_start: 0.8691 (tp) cc_final: 0.8428 (tt) outliers start: 7 outliers final: 4 residues processed: 229 average time/residue: 1.0711 time to fit residues: 261.8184 Evaluate side-chains 140 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 264 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 255 ASN A 311 ASN B 91 HIS B 220 GLN B 259 GLN R 154 HIS R 178 HIS R 304 HIS S 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8636 Z= 0.302 Angle : 0.686 10.862 11748 Z= 0.360 Chirality : 0.046 0.173 1370 Planarity : 0.005 0.044 1463 Dihedral : 7.367 68.942 1359 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.68 % Allowed : 13.09 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.24), residues: 1101 helix: -0.51 (0.28), residues: 343 sheet: -0.93 (0.29), residues: 271 loop : -1.72 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.006 0.002 HIS B 142 PHE 0.018 0.002 PHE B 241 TYR 0.027 0.002 TYR S 178 ARG 0.004 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 0.995 Fit side-chains REVERT: A 308 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 333 GLN cc_start: 0.8219 (tp40) cc_final: 0.7783 (tm-30) REVERT: B 13 GLN cc_start: 0.7221 (mt0) cc_final: 0.6895 (tt0) REVERT: B 217 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8128 (pmm) REVERT: B 292 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: R 308 MET cc_start: 0.6942 (mmp) cc_final: 0.6049 (tmt) REVERT: R 353 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7139 (tp) outliers start: 39 outliers final: 15 residues processed: 173 average time/residue: 0.9404 time to fit residues: 175.7257 Evaluate side-chains 141 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0060 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS R 270 HIS S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8636 Z= 0.248 Angle : 0.594 10.416 11748 Z= 0.312 Chirality : 0.043 0.199 1370 Planarity : 0.004 0.046 1463 Dihedral : 6.947 65.407 1355 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.80 % Allowed : 15.25 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.24), residues: 1101 helix: -0.10 (0.29), residues: 346 sheet: -0.68 (0.29), residues: 271 loop : -1.70 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 279 HIS 0.007 0.001 HIS B 142 PHE 0.017 0.002 PHE B 241 TYR 0.024 0.002 TYR S 215 ARG 0.006 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 0.973 Fit side-chains REVERT: A 333 GLN cc_start: 0.8239 (tp40) cc_final: 0.7641 (tm-30) REVERT: B 13 GLN cc_start: 0.7144 (mt0) cc_final: 0.6850 (tt0) REVERT: B 188 MET cc_start: 0.8740 (mmm) cc_final: 0.8516 (mmm) REVERT: B 217 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8136 (pmm) REVERT: B 292 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: C 63 GLU cc_start: 0.6812 (tp30) cc_final: 0.6526 (tp30) REVERT: R 308 MET cc_start: 0.6931 (mmp) cc_final: 0.6036 (tmt) REVERT: R 353 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7174 (tp) REVERT: S 84 THR cc_start: 0.8342 (m) cc_final: 0.8041 (p) REVERT: S 128 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.7805 (mmm) outliers start: 40 outliers final: 17 residues processed: 156 average time/residue: 0.9882 time to fit residues: 166.0078 Evaluate side-chains 144 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 322 HIS A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN S 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8636 Z= 0.244 Angle : 0.575 10.998 11748 Z= 0.302 Chirality : 0.042 0.204 1370 Planarity : 0.004 0.049 1463 Dihedral : 6.669 62.518 1354 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.16 % Allowed : 16.09 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1101 helix: 0.03 (0.29), residues: 349 sheet: -0.62 (0.30), residues: 275 loop : -1.64 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 279 HIS 0.008 0.001 HIS B 142 PHE 0.025 0.002 PHE R 237 TYR 0.022 0.002 TYR S 178 ARG 0.004 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 132 time to evaluate : 0.877 Fit side-chains REVERT: A 24 ARG cc_start: 0.7873 (ttp-170) cc_final: 0.7632 (ttm-80) REVERT: A 308 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8115 (mt-10) REVERT: A 316 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 333 GLN cc_start: 0.8266 (tp40) cc_final: 0.7701 (tm-30) REVERT: B 13 GLN cc_start: 0.7175 (mt0) cc_final: 0.6897 (tt0) REVERT: B 217 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8148 (pmm) REVERT: B 234 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: C 58 GLU cc_start: 0.7840 (pm20) cc_final: 0.7385 (pm20) REVERT: C 63 GLU cc_start: 0.6846 (tp30) cc_final: 0.6466 (tp30) REVERT: R 308 MET cc_start: 0.6978 (mmp) cc_final: 0.6105 (tmt) REVERT: R 353 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7217 (tp) REVERT: S 84 THR cc_start: 0.8327 (m) cc_final: 0.8012 (p) REVERT: S 128 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.7788 (mmm) outliers start: 43 outliers final: 23 residues processed: 154 average time/residue: 0.9667 time to fit residues: 160.4715 Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 LYS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 59 ASN R 178 HIS R 389 ASN S 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8636 Z= 0.195 Angle : 0.546 11.009 11748 Z= 0.285 Chirality : 0.041 0.229 1370 Planarity : 0.003 0.047 1463 Dihedral : 6.382 60.490 1352 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.92 % Allowed : 17.77 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1101 helix: 0.26 (0.29), residues: 346 sheet: -0.46 (0.31), residues: 270 loop : -1.61 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS B 142 PHE 0.024 0.001 PHE R 237 TYR 0.018 0.001 TYR S 178 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 0.932 Fit side-chains REVERT: A 24 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7611 (ttm-80) REVERT: A 316 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 333 GLN cc_start: 0.8259 (tp40) cc_final: 0.7790 (tm-30) REVERT: B 13 GLN cc_start: 0.7155 (mt0) cc_final: 0.6899 (tt0) REVERT: B 217 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8157 (pmm) REVERT: B 234 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: C 11 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 21 MET cc_start: 0.8206 (tpp) cc_final: 0.7893 (mpp) REVERT: C 58 GLU cc_start: 0.7819 (pm20) cc_final: 0.7365 (pm20) REVERT: R 308 MET cc_start: 0.6956 (mmp) cc_final: 0.6087 (tmt) outliers start: 41 outliers final: 20 residues processed: 164 average time/residue: 0.9728 time to fit residues: 171.8516 Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 LYS Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8636 Z= 0.137 Angle : 0.515 12.479 11748 Z= 0.265 Chirality : 0.040 0.249 1370 Planarity : 0.003 0.045 1463 Dihedral : 5.960 56.729 1352 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 19.81 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.84 (0.25), residues: 1101 helix: 0.43 (0.29), residues: 349 sheet: -0.35 (0.30), residues: 283 loop : -1.40 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 279 HIS 0.003 0.001 HIS R 143 PHE 0.029 0.001 PHE R 237 TYR 0.010 0.001 TYR S 178 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.023 Fit side-chains REVERT: A 24 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7547 (ttm-80) REVERT: A 316 THR cc_start: 0.8854 (m) cc_final: 0.8600 (p) REVERT: A 333 GLN cc_start: 0.8278 (tp40) cc_final: 0.7727 (tm-30) REVERT: B 13 GLN cc_start: 0.7147 (mt0) cc_final: 0.6911 (tt0) REVERT: B 214 ARG cc_start: 0.8417 (mtt180) cc_final: 0.8216 (mtt180) REVERT: B 217 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8164 (pmm) REVERT: R 308 MET cc_start: 0.6812 (mmp) cc_final: 0.6010 (tmt) REVERT: R 365 TYR cc_start: 0.7468 (t80) cc_final: 0.7088 (t80) outliers start: 28 outliers final: 14 residues processed: 153 average time/residue: 1.0122 time to fit residues: 166.7005 Evaluate side-chains 147 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8636 Z= 0.119 Angle : 0.493 8.328 11748 Z= 0.256 Chirality : 0.040 0.258 1370 Planarity : 0.003 0.042 1463 Dihedral : 5.716 53.459 1352 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.64 % Allowed : 21.61 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.64 (0.25), residues: 1101 helix: 0.64 (0.29), residues: 351 sheet: -0.21 (0.31), residues: 278 loop : -1.32 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 279 HIS 0.003 0.001 HIS R 143 PHE 0.026 0.001 PHE R 237 TYR 0.009 0.001 TYR S 178 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.017 Fit side-chains REVERT: A 316 THR cc_start: 0.8801 (m) cc_final: 0.8545 (p) REVERT: A 333 GLN cc_start: 0.8277 (tp40) cc_final: 0.7744 (tm-30) REVERT: B 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8253 (pmm) REVERT: R 308 MET cc_start: 0.6755 (mmp) cc_final: 0.6034 (tmt) REVERT: R 365 TYR cc_start: 0.7391 (t80) cc_final: 0.7092 (t80) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 0.9839 time to fit residues: 161.1891 Evaluate side-chains 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8636 Z= 0.153 Angle : 0.523 12.883 11748 Z= 0.268 Chirality : 0.041 0.256 1370 Planarity : 0.003 0.041 1463 Dihedral : 5.776 52.556 1352 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.68 % Allowed : 22.45 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1101 helix: 0.68 (0.29), residues: 358 sheet: -0.22 (0.31), residues: 284 loop : -1.37 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.026 0.001 PHE R 237 TYR 0.014 0.001 TYR S 178 ARG 0.010 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.901 Fit side-chains REVERT: A 316 THR cc_start: 0.8799 (m) cc_final: 0.8542 (p) REVERT: B 217 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8257 (pmm) REVERT: R 365 TYR cc_start: 0.7452 (t80) cc_final: 0.7124 (t80) outliers start: 14 outliers final: 11 residues processed: 140 average time/residue: 0.9745 time to fit residues: 147.0219 Evaluate side-chains 139 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8636 Z= 0.126 Angle : 0.514 12.478 11748 Z= 0.261 Chirality : 0.040 0.252 1370 Planarity : 0.003 0.040 1463 Dihedral : 5.582 56.398 1352 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.16 % Allowed : 22.45 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.35 (0.25), residues: 1101 helix: 0.97 (0.29), residues: 352 sheet: -0.04 (0.31), residues: 281 loop : -1.26 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 279 HIS 0.003 0.001 HIS B 142 PHE 0.030 0.001 PHE R 237 TYR 0.009 0.001 TYR S 178 ARG 0.009 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8307 (pmm) REVERT: R 365 TYR cc_start: 0.7396 (t80) cc_final: 0.7064 (t80) outliers start: 18 outliers final: 11 residues processed: 143 average time/residue: 0.9762 time to fit residues: 150.7550 Evaluate side-chains 140 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 113 GLN S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8636 Z= 0.268 Angle : 0.592 12.630 11748 Z= 0.308 Chirality : 0.043 0.205 1370 Planarity : 0.004 0.044 1463 Dihedral : 6.175 56.704 1352 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.68 % Allowed : 23.89 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1101 helix: 0.84 (0.29), residues: 352 sheet: -0.25 (0.31), residues: 284 loop : -1.43 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 47 HIS 0.009 0.001 HIS B 142 PHE 0.026 0.002 PHE R 237 TYR 0.027 0.002 TYR S 178 ARG 0.009 0.001 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.947 Fit side-chains REVERT: A 316 THR cc_start: 0.8833 (m) cc_final: 0.8592 (p) REVERT: A 337 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: B 217 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8191 (pmm) REVERT: R 365 TYR cc_start: 0.7572 (t80) cc_final: 0.7252 (t80) REVERT: S 206 ARG cc_start: 0.8026 (ppt90) cc_final: 0.7394 (ptm160) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 1.0698 time to fit residues: 151.5752 Evaluate side-chains 137 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107465 restraints weight = 11694.548| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.96 r_work: 0.3304 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8636 Z= 0.145 Angle : 0.533 12.411 11748 Z= 0.273 Chirality : 0.040 0.169 1370 Planarity : 0.003 0.043 1463 Dihedral : 5.730 55.352 1352 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 24.37 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.42 (0.25), residues: 1101 helix: 1.01 (0.29), residues: 349 sheet: -0.11 (0.31), residues: 279 loop : -1.35 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.028 0.001 PHE R 237 TYR 0.011 0.001 TYR A 287 ARG 0.009 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3381.79 seconds wall clock time: 60 minutes 42.27 seconds (3642.27 seconds total)