Starting phenix.real_space_refine on Fri Mar 15 07:30:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/03_2024/6x1a_21994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/03_2024/6x1a_21994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/03_2024/6x1a_21994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/03_2024/6x1a_21994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/03_2024/6x1a_21994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/03_2024/6x1a_21994_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 849 atoms to isotropic. 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 59 5.16 5 C 6444 2.51 5 N 1746 2.21 5 O 1890 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 GLU 145": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R GLU 262": "OE1" <-> "OE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R GLU 387": "OE1" <-> "OE2" Residue "R GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2873 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3270 Unusual residues: {'UK4': 1} Classifications: {'peptide': 390, 'undetermined': 1, 'water': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375, None: 24} Not linked: pdbres="GLU R 423 " pdbres="UK4 R 501 " Not linked: pdbres="UK4 R 501 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " Not linked: pdbres="HOH R 602 " pdbres="HOH R 603 " Not linked: pdbres="HOH R 603 " pdbres="HOH R 604 " ... (remaining 19 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.66, per 1000 atoms: 0.56 Number of scatterers: 10140 At special positions: 0 Unit cell: (112.05, 99.6, 164.34, 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 59 16.00 F 1 9.00 O 1890 8.00 N 1746 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 10 sheets defined 38.9% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.565A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.685A pdb=" N ASN A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.803A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.541A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.892A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 4.244A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 383 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 388 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.875A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (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 'G' and resid 7 through 22 removed outlier: 3.633A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 33 No H-bonds generated for 'chain 'G' and resid 30 through 33' Processing helix chain 'G' and resid 37 through 41 removed outlier: 3.519A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 37 through 41' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.619A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 166 Processing helix chain 'R' and resid 175 through 200 Processing helix chain 'R' and resid 211 through 222 removed outlier: 3.521A pdb=" N TRP R 214 " --> pdb=" O GLN R 211 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 217 " --> pdb=" O TRP R 214 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER R 219 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR R 220 " --> pdb=" O LEU R 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 255 Processing helix chain 'R' and resid 262 through 273 removed outlier: 3.766A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 290 removed outlier: 3.733A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.952A pdb=" N ILE R 286 " --> pdb=" O PRO R 283 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS R 288 " --> pdb=" O GLY R 285 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU R 290 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 336 removed outlier: 3.740A pdb=" N ARG R 310 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.640A pdb=" N GLY R 318 " --> pdb=" O PHE R 315 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL R 319 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 321 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 323 " --> pdb=" O ASN R 320 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL R 325 " --> pdb=" O LEU R 322 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL R 332 " --> pdb=" O CYS R 329 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS R 334 " --> pdb=" O VAL R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 360 removed outlier: 3.519A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 370 removed outlier: 3.586A pdb=" N VAL R 365 " --> pdb=" O THR R 362 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE R 367 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 401 removed outlier: 3.670A pdb=" N ILE R 382 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 385 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR R 386 " --> pdb=" O LYS R 383 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU R 388 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR R 391 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER R 392 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY R 395 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE R 400 " --> pdb=" O MET R 397 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU R 401 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 418 removed outlier: 3.513A pdb=" N TRP R 417 " --> pdb=" O PHE R 413 " (cutoff:3.500A) Processing helix chain 'R' and resid 420 through 422 No H-bonds generated for 'chain 'R' and resid 420 through 422' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.454A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.397A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.296A 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 151 removed outlier: 6.669A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.991A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 265 removed outlier: 4.515A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.408A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.864A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.223A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 912 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: 2.75 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1656 1.27 - 1.40: 2709 1.40 - 1.54: 5847 1.54 - 1.68: 61 1.68 - 1.81: 79 Bond restraints: 10352 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.424 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.529 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C PRO A 115 " pdb=" N PRO A 116 " ideal model delta sigma weight residual 1.330 1.381 -0.051 1.19e-02 7.06e+03 1.82e+01 bond pdb=" C ASP B 27 " pdb=" N ALA B 28 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.25e-02 6.40e+03 1.66e+01 bond pdb=" C PHE A 142 " pdb=" N PRO A 143 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.18e-02 7.18e+03 1.64e+01 ... (remaining 10347 not shown) Histogram of bond angle deviations from ideal: 89.64 - 107.70: 410 107.70 - 125.75: 13436 125.75 - 143.81: 197 143.81 - 161.86: 0 161.86 - 179.92: 1 Bond angle restraints: 14044 Sorted by residual: angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 112.04 101.46 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" N PRO A 138 " pdb=" CA PRO A 138 " pdb=" C PRO A 138 " ideal model delta sigma weight residual 113.53 103.10 10.43 1.39e+00 5.18e-01 5.63e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.42 17.84 3.00e+00 1.11e-01 3.54e+01 angle pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta sigma weight residual 120.38 125.97 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C VAL A 191 " pdb=" N PRO A 192 " pdb=" CA PRO A 192 " ideal model delta sigma weight residual 119.76 125.25 -5.49 1.03e+00 9.43e-01 2.84e+01 ... (remaining 14039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5457 17.47 - 34.95: 518 34.95 - 52.42: 138 52.42 - 69.89: 27 69.89 - 87.36: 13 Dihedral angle restraints: 6153 sinusoidal: 2457 harmonic: 3696 Sorted by residual: dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 173.00 -80.00 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CA VAL A 114 " pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN A 292 " pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta harmonic sigma weight residual -180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1262 0.071 - 0.143: 201 0.143 - 0.214: 55 0.214 - 0.286: 20 0.286 - 0.357: 5 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA VAL A 214 " pdb=" N VAL A 214 " pdb=" C VAL A 214 " pdb=" CB VAL A 214 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA LYS A 100 " pdb=" N LYS A 100 " pdb=" C LYS A 100 " pdb=" CB LYS A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1540 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 364 " 0.068 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.026 2.00e-02 2.50e+03 pdb=" N CYS A 365 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 322 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C GLU A 322 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 323 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 61 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C PHE G 61 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE G 61 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG G 62 " 0.014 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 289 2.69 - 3.24: 10118 3.24 - 3.80: 16021 3.80 - 4.35: 23096 4.35 - 4.90: 35867 Nonbonded interactions: 85391 Sorted by model distance: nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.140 2.440 nonbonded pdb=" O HOH R 603 " pdb=" O HOH R 617 " model vdw 2.230 2.440 nonbonded pdb=" O GLN R 234 " pdb=" O HOH R 601 " model vdw 2.233 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR R 152 " pdb=" O HOH R 602 " model vdw 2.261 2.440 ... (remaining 85386 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 5.720 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.280 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 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 : 0.006 0.111 10352 Z= 0.402 Angle : 0.926 17.839 14044 Z= 0.655 Chirality : 0.066 0.357 1543 Planarity : 0.004 0.051 1794 Dihedral : 15.442 87.364 3743 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.79 % Allowed : 15.97 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1246 helix: -2.54 (0.18), residues: 498 sheet: -1.43 (0.34), residues: 193 loop : -1.72 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 149 PHE 0.012 0.001 PHE A 219 TYR 0.025 0.001 TYR B 145 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.2248 (ptt) cc_final: 0.1891 (mtm) REVERT: A 222 PHE cc_start: 0.7406 (m-80) cc_final: 0.7150 (m-80) REVERT: A 265 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6997 (ttt-90) REVERT: A 358 TYR cc_start: 0.6807 (m-80) cc_final: 0.6163 (m-80) REVERT: B 38 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5043 (p0) REVERT: B 44 GLN cc_start: 0.6341 (mp10) cc_final: 0.5987 (mp10) REVERT: B 75 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7181 (tp40) REVERT: B 142 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5731 (m-70) REVERT: B 228 ASP cc_start: 0.7773 (m-30) cc_final: 0.7539 (m-30) REVERT: B 322 ASP cc_start: 0.5199 (OUTLIER) cc_final: 0.4932 (t70) REVERT: G 32 LYS cc_start: 0.6958 (mmmt) cc_final: 0.6483 (tptt) REVERT: N 43 LYS cc_start: 0.6071 (tmtt) cc_final: 0.5806 (tmtt) REVERT: N 78 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7367 (m) REVERT: R 62 CYS cc_start: 0.1138 (OUTLIER) cc_final: 0.0588 (m) REVERT: R 67 ASP cc_start: 0.7114 (p0) cc_final: 0.6785 (p0) REVERT: R 170 ARG cc_start: 0.5551 (ttt180) cc_final: 0.5301 (tpp80) REVERT: R 414 ARG cc_start: 0.5815 (mmt-90) cc_final: 0.5337 (mmm160) outliers start: 41 outliers final: 17 residues processed: 197 average time/residue: 1.0365 time to fit residues: 221.0505 Evaluate side-chains 145 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 64 HIS A 112 ASN A 136 ASN A 170 GLN A 218 ASN A 236 GLN A 377 ASN A 390 GLN B 16 ASN B 36 ASN B 88 ASN B 110 ASN B 125 ASN B 155 ASN B 176 GLN B 183 HIS B 295 ASN B 340 ASN G 18 GLN G 24 ASN N 1 GLN N 31 ASN N 35 ASN N 77 ASN R 45 GLN R 177 ASN R 263 GLN R 302 ASN R 304 ASN R 394 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10352 Z= 0.166 Angle : 0.563 10.312 14044 Z= 0.299 Chirality : 0.041 0.153 1543 Planarity : 0.004 0.051 1794 Dihedral : 6.297 59.846 1439 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.71 % Allowed : 17.64 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.22), residues: 1246 helix: -1.01 (0.22), residues: 493 sheet: -0.93 (0.32), residues: 222 loop : -1.18 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 64 PHE 0.011 0.001 PHE A 212 TYR 0.028 0.001 TYR R 148 ARG 0.008 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 130 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.1703 (ptt) cc_final: 0.1494 (mtm) REVERT: A 265 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6214 (ttt-90) REVERT: A 267 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7743 (tp-100) REVERT: A 358 TYR cc_start: 0.6815 (m-80) cc_final: 0.6084 (m-80) REVERT: B 44 GLN cc_start: 0.6292 (mp10) cc_final: 0.5940 (mp10) REVERT: B 59 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5729 (t80) REVERT: B 124 TYR cc_start: 0.5382 (m-80) cc_final: 0.5059 (m-80) REVERT: B 142 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.4883 (m-70) REVERT: B 205 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7021 (p0) REVERT: B 228 ASP cc_start: 0.7835 (m-30) cc_final: 0.7584 (m-30) REVERT: B 261 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7669 (mp) REVERT: G 32 LYS cc_start: 0.6955 (mmmt) cc_final: 0.6496 (tptt) REVERT: N 43 LYS cc_start: 0.6091 (tmtt) cc_final: 0.5857 (mmtp) REVERT: N 46 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6600 (mm-30) REVERT: N 89 GLU cc_start: 0.6752 (mp0) cc_final: 0.6370 (mp0) REVERT: R 50 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5378 (mp) REVERT: R 67 ASP cc_start: 0.7012 (p0) cc_final: 0.6660 (p0) REVERT: R 170 ARG cc_start: 0.5537 (ttt180) cc_final: 0.5259 (tpp80) REVERT: R 397 MET cc_start: 0.6491 (mmt) cc_final: 0.6268 (mmp) REVERT: R 411 LEU cc_start: 0.6738 (mt) cc_final: 0.6499 (mt) REVERT: R 414 ARG cc_start: 0.5639 (mmt-90) cc_final: 0.5217 (mmm160) outliers start: 51 outliers final: 24 residues processed: 176 average time/residue: 1.0368 time to fit residues: 198.3497 Evaluate side-chains 140 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 261 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 187 GLN A 387 HIS B 110 ASN B 155 ASN B 268 ASN N 3 GLN R 45 GLN R 212 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10352 Z= 0.134 Angle : 0.516 9.976 14044 Z= 0.269 Chirality : 0.040 0.154 1543 Planarity : 0.004 0.050 1794 Dihedral : 5.631 56.761 1424 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.71 % Allowed : 19.76 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1246 helix: -0.39 (0.23), residues: 493 sheet: -0.54 (0.32), residues: 223 loop : -0.95 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 72 HIS 0.003 0.001 HIS A 220 PHE 0.010 0.001 PHE A 212 TYR 0.028 0.001 TYR R 148 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.1756 (ptt) cc_final: 0.1547 (mtm) REVERT: A 265 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6263 (ttt-90) REVERT: A 358 TYR cc_start: 0.6867 (m-80) cc_final: 0.6089 (m-80) REVERT: B 38 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5215 (p0) REVERT: B 44 GLN cc_start: 0.6264 (mp10) cc_final: 0.5908 (mp10) REVERT: B 59 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.5720 (t80) REVERT: B 124 TYR cc_start: 0.5437 (m-80) cc_final: 0.5142 (m-80) REVERT: B 142 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.5104 (m-70) REVERT: B 205 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6889 (p0) REVERT: B 217 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.6133 (pmm) REVERT: B 219 ARG cc_start: 0.6696 (ttm170) cc_final: 0.6373 (ttm110) REVERT: B 228 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: B 261 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7656 (mp) REVERT: B 266 HIS cc_start: 0.6079 (t-170) cc_final: 0.5778 (t70) REVERT: G 32 LYS cc_start: 0.6957 (mmmt) cc_final: 0.6491 (tptt) REVERT: N 43 LYS cc_start: 0.6277 (tmtt) cc_final: 0.5914 (mmtt) REVERT: N 46 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6583 (mm-30) REVERT: N 91 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7340 (t) REVERT: R 50 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5534 (mp) REVERT: R 67 ASP cc_start: 0.7063 (p0) cc_final: 0.6691 (p0) REVERT: R 170 ARG cc_start: 0.5486 (ttt180) cc_final: 0.5201 (tpp80) REVERT: R 346 LYS cc_start: 0.5772 (mttp) cc_final: 0.5414 (mtmt) REVERT: R 397 MET cc_start: 0.6436 (mmt) cc_final: 0.6221 (mmp) REVERT: R 411 LEU cc_start: 0.6809 (mt) cc_final: 0.6592 (mt) REVERT: R 414 ARG cc_start: 0.5668 (mmt-90) cc_final: 0.5286 (mmm160) outliers start: 51 outliers final: 25 residues processed: 167 average time/residue: 1.0285 time to fit residues: 186.7771 Evaluate side-chains 149 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 110 ASN B 155 ASN B 268 ASN G 18 GLN N 1 GLN N 3 GLN N 5 GLN N 82 GLN R 45 GLN R 212 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10352 Z= 0.268 Angle : 0.665 13.702 14044 Z= 0.347 Chirality : 0.045 0.160 1543 Planarity : 0.005 0.064 1794 Dihedral : 6.226 56.358 1423 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.82 % Allowed : 19.11 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1246 helix: -0.49 (0.23), residues: 487 sheet: -0.46 (0.33), residues: 231 loop : -0.82 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 243 HIS 0.011 0.002 HIS A 220 PHE 0.014 0.002 PHE B 199 TYR 0.028 0.002 TYR R 148 ARG 0.007 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 114 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6171 (ttt-90) REVERT: A 357 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8283 (p90) REVERT: B 44 GLN cc_start: 0.6212 (mp10) cc_final: 0.5842 (mp10) REVERT: B 51 LEU cc_start: 0.6806 (mt) cc_final: 0.6593 (mm) REVERT: B 59 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.5841 (t80) REVERT: B 142 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6110 (m-70) REVERT: B 217 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6169 (pmm) REVERT: B 228 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: B 261 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7775 (mp) REVERT: G 32 LYS cc_start: 0.7156 (mmmt) cc_final: 0.6614 (tptt) REVERT: N 43 LYS cc_start: 0.6134 (tmtt) cc_final: 0.5882 (mmtp) REVERT: N 46 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6608 (mm-30) REVERT: N 77 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6847 (m-40) REVERT: N 78 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7406 (m) REVERT: R 50 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5554 (mp) REVERT: R 67 ASP cc_start: 0.7056 (p0) cc_final: 0.6721 (p0) REVERT: R 170 ARG cc_start: 0.5631 (ttt180) cc_final: 0.5401 (tpp80) REVERT: R 346 LYS cc_start: 0.5809 (mttp) cc_final: 0.5414 (mtmt) REVERT: R 397 MET cc_start: 0.6527 (mmt) cc_final: 0.6321 (mmp) REVERT: R 414 ARG cc_start: 0.5676 (mmt-90) cc_final: 0.5249 (mmm160) outliers start: 63 outliers final: 33 residues processed: 166 average time/residue: 0.9653 time to fit residues: 175.2359 Evaluate side-chains 150 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10352 Z= 0.172 Angle : 0.557 11.771 14044 Z= 0.291 Chirality : 0.041 0.158 1543 Planarity : 0.004 0.061 1794 Dihedral : 5.900 58.338 1422 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.17 % Allowed : 21.14 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1246 helix: -0.20 (0.23), residues: 490 sheet: -0.31 (0.34), residues: 224 loop : -0.72 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.010 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.025 0.002 TYR R 148 ARG 0.010 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 LYS cc_start: 0.1365 (OUTLIER) cc_final: 0.1144 (pptt) REVERT: A 265 ARG cc_start: 0.7041 (mtp85) cc_final: 0.6112 (ttt-90) REVERT: B 44 GLN cc_start: 0.6235 (mp10) cc_final: 0.5874 (mp10) REVERT: B 59 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.5772 (t80) REVERT: B 142 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.5941 (m-70) REVERT: B 205 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7078 (p0) REVERT: B 217 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6144 (pmm) REVERT: B 219 ARG cc_start: 0.6673 (ttm170) cc_final: 0.6410 (ttm110) REVERT: B 228 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: B 261 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 304 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6126 (mtm180) REVERT: G 32 LYS cc_start: 0.7071 (mmmt) cc_final: 0.6579 (tptt) REVERT: G 59 ASN cc_start: 0.4835 (OUTLIER) cc_final: 0.4189 (t0) REVERT: N 43 LYS cc_start: 0.6256 (tmtt) cc_final: 0.5893 (mmtt) REVERT: N 46 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6586 (mm-30) REVERT: N 78 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7382 (m) REVERT: R 50 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5514 (mp) REVERT: R 67 ASP cc_start: 0.7003 (p0) cc_final: 0.6683 (p0) REVERT: R 170 ARG cc_start: 0.5569 (ttt180) cc_final: 0.5338 (tpp80) REVERT: R 346 LYS cc_start: 0.5754 (mttp) cc_final: 0.5399 (mtmt) REVERT: R 397 MET cc_start: 0.6562 (mmt) cc_final: 0.6341 (mmp) REVERT: R 414 ARG cc_start: 0.5612 (mmt-90) cc_final: 0.5184 (mmm-85) outliers start: 56 outliers final: 30 residues processed: 161 average time/residue: 0.9713 time to fit residues: 171.1198 Evaluate side-chains 151 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 7.9990 chunk 109 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.0170 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 110 ASN B 155 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10352 Z= 0.195 Angle : 0.586 11.850 14044 Z= 0.305 Chirality : 0.042 0.203 1543 Planarity : 0.004 0.061 1794 Dihedral : 5.884 58.819 1420 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.72 % Allowed : 21.51 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.24), residues: 1246 helix: -0.13 (0.23), residues: 489 sheet: -0.27 (0.34), residues: 222 loop : -0.64 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 72 HIS 0.010 0.001 HIS A 220 PHE 0.027 0.002 PHE A 222 TYR 0.026 0.002 TYR R 148 ARG 0.010 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 112 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 LYS cc_start: 0.1320 (OUTLIER) cc_final: 0.1086 (pptt) REVERT: A 265 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6106 (ttt-90) REVERT: B 44 GLN cc_start: 0.6211 (mp10) cc_final: 0.5861 (mp10) REVERT: B 59 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5735 (t80) REVERT: B 142 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6123 (m-70) REVERT: B 205 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 217 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6194 (pmm) REVERT: B 228 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: B 261 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 304 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6146 (mtm180) REVERT: G 32 LYS cc_start: 0.7116 (mmmt) cc_final: 0.6614 (tptt) REVERT: G 59 ASN cc_start: 0.4817 (OUTLIER) cc_final: 0.4159 (t0) REVERT: N 43 LYS cc_start: 0.6250 (tmtt) cc_final: 0.5877 (mmtt) REVERT: N 46 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6595 (mm-30) REVERT: N 78 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7367 (m) REVERT: R 50 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5500 (mp) REVERT: R 67 ASP cc_start: 0.6953 (p0) cc_final: 0.6633 (p0) REVERT: R 170 ARG cc_start: 0.5575 (ttt180) cc_final: 0.5349 (tpp80) REVERT: R 292 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.5164 (mt-10) REVERT: R 346 LYS cc_start: 0.5591 (mttp) cc_final: 0.5279 (mtmt) REVERT: R 397 MET cc_start: 0.6567 (mmt) cc_final: 0.6348 (mmp) REVERT: R 414 ARG cc_start: 0.5632 (mmt-90) cc_final: 0.5189 (mmm-85) outliers start: 62 outliers final: 38 residues processed: 161 average time/residue: 1.0006 time to fit residues: 175.9146 Evaluate side-chains 159 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 109 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN B 266 HIS B 268 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10352 Z= 0.192 Angle : 0.577 11.955 14044 Z= 0.301 Chirality : 0.042 0.186 1543 Planarity : 0.004 0.060 1794 Dihedral : 5.898 58.885 1420 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.72 % Allowed : 21.24 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.24), residues: 1246 helix: -0.14 (0.23), residues: 491 sheet: -0.29 (0.33), residues: 232 loop : -0.55 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 72 HIS 0.011 0.001 HIS A 220 PHE 0.041 0.002 PHE A 222 TYR 0.026 0.002 TYR R 148 ARG 0.011 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 115 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6111 (ttt-90) REVERT: B 44 GLN cc_start: 0.6271 (mp10) cc_final: 0.5914 (mp10) REVERT: B 59 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.5734 (t80) REVERT: B 142 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6049 (m-70) REVERT: B 205 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7081 (p0) REVERT: B 217 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6231 (pmm) REVERT: B 228 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: B 261 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7765 (mp) REVERT: B 304 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6127 (mtm180) REVERT: B 325 MET cc_start: 0.5114 (mpp) cc_final: 0.4353 (ptt) REVERT: G 32 LYS cc_start: 0.7101 (mmmt) cc_final: 0.6599 (tptt) REVERT: G 59 ASN cc_start: 0.4819 (OUTLIER) cc_final: 0.4120 (t0) REVERT: N 43 LYS cc_start: 0.6245 (tmtt) cc_final: 0.5875 (mmtt) REVERT: N 46 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6604 (mm-30) REVERT: N 78 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7367 (m) REVERT: R 67 ASP cc_start: 0.6954 (p0) cc_final: 0.6621 (p0) REVERT: R 170 ARG cc_start: 0.5578 (ttt180) cc_final: 0.5349 (tpp80) REVERT: R 292 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.5110 (mt-10) REVERT: R 346 LYS cc_start: 0.5600 (mttp) cc_final: 0.5286 (mtmt) REVERT: R 397 MET cc_start: 0.6583 (mmt) cc_final: 0.6354 (mmp) REVERT: R 414 ARG cc_start: 0.5605 (mmt-90) cc_final: 0.5167 (mmm-85) outliers start: 62 outliers final: 39 residues processed: 163 average time/residue: 0.9811 time to fit residues: 174.4472 Evaluate side-chains 159 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 110 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10352 Z= 0.170 Angle : 0.555 11.398 14044 Z= 0.289 Chirality : 0.042 0.156 1543 Planarity : 0.004 0.059 1794 Dihedral : 5.786 59.610 1420 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.36 % Allowed : 21.88 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.24), residues: 1246 helix: -0.04 (0.23), residues: 491 sheet: -0.26 (0.33), residues: 232 loop : -0.47 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 72 HIS 0.004 0.001 HIS A 220 PHE 0.067 0.002 PHE A 222 TYR 0.026 0.002 TYR R 148 ARG 0.014 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 113 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6125 (ttt-90) REVERT: B 44 GLN cc_start: 0.6265 (mp10) cc_final: 0.5916 (mp10) REVERT: B 59 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5741 (t80) REVERT: B 142 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.5933 (m-70) REVERT: B 205 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7064 (p0) REVERT: B 217 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6232 (pmm) REVERT: B 228 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: B 261 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7740 (mp) REVERT: B 304 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6114 (mtm180) REVERT: B 325 MET cc_start: 0.5081 (mpp) cc_final: 0.4517 (ptt) REVERT: G 32 LYS cc_start: 0.7057 (mmmt) cc_final: 0.6579 (tptt) REVERT: G 59 ASN cc_start: 0.4805 (OUTLIER) cc_final: 0.4106 (t0) REVERT: N 43 LYS cc_start: 0.6236 (tmtt) cc_final: 0.5870 (mmtt) REVERT: N 46 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6598 (mm-30) REVERT: N 78 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (m) REVERT: R 67 ASP cc_start: 0.6913 (p0) cc_final: 0.6577 (p0) REVERT: R 170 ARG cc_start: 0.5551 (ttt180) cc_final: 0.5314 (tpp80) REVERT: R 292 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5069 (mt-10) REVERT: R 346 LYS cc_start: 0.5709 (mttp) cc_final: 0.5403 (mtmt) REVERT: R 397 MET cc_start: 0.6571 (mmt) cc_final: 0.6335 (mmp) REVERT: R 414 ARG cc_start: 0.5601 (mmt-90) cc_final: 0.5208 (mmm160) outliers start: 58 outliers final: 35 residues processed: 156 average time/residue: 0.9794 time to fit residues: 166.1653 Evaluate side-chains 158 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 113 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.0050 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10352 Z= 0.139 Angle : 0.535 12.238 14044 Z= 0.278 Chirality : 0.040 0.158 1543 Planarity : 0.004 0.060 1794 Dihedral : 5.569 58.551 1419 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.43 % Allowed : 22.62 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.24), residues: 1246 helix: 0.13 (0.24), residues: 492 sheet: -0.29 (0.34), residues: 215 loop : -0.30 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.039 0.002 HIS A 220 PHE 0.039 0.001 PHE A 222 TYR 0.026 0.001 TYR R 148 ARG 0.016 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 265 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6054 (ttt-90) REVERT: B 44 GLN cc_start: 0.6261 (mp10) cc_final: 0.5915 (mp10) REVERT: B 59 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.5701 (t80) REVERT: B 142 HIS cc_start: 0.6753 (OUTLIER) cc_final: 0.5745 (m-70) REVERT: B 205 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7019 (p0) REVERT: B 217 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6147 (pmm) REVERT: B 228 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: B 261 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7730 (mp) REVERT: B 304 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6093 (mtm180) REVERT: B 325 MET cc_start: 0.5009 (mpp) cc_final: 0.4661 (ptt) REVERT: G 32 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6493 (tptt) REVERT: G 59 ASN cc_start: 0.4767 (OUTLIER) cc_final: 0.4080 (t0) REVERT: N 43 LYS cc_start: 0.6196 (tmtt) cc_final: 0.5843 (mmtt) REVERT: N 46 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6590 (mm-30) REVERT: R 67 ASP cc_start: 0.6887 (p0) cc_final: 0.6561 (p0) REVERT: R 93 SER cc_start: 0.6316 (OUTLIER) cc_final: 0.6049 (p) REVERT: R 170 ARG cc_start: 0.5537 (ttt180) cc_final: 0.5294 (tpp80) REVERT: R 292 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5047 (mt-10) REVERT: R 346 LYS cc_start: 0.5741 (mttp) cc_final: 0.5447 (mtmt) REVERT: R 372 ASP cc_start: 0.6747 (m-30) cc_final: 0.6461 (t0) REVERT: R 397 MET cc_start: 0.6437 (mmt) cc_final: 0.6232 (mmp) REVERT: R 414 ARG cc_start: 0.5578 (mmt-90) cc_final: 0.5202 (mmm160) outliers start: 48 outliers final: 26 residues processed: 150 average time/residue: 0.9367 time to fit residues: 153.9727 Evaluate side-chains 144 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 50.0000 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.0020 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10352 Z= 0.137 Angle : 0.528 10.456 14044 Z= 0.274 Chirality : 0.040 0.157 1543 Planarity : 0.004 0.072 1794 Dihedral : 5.478 57.770 1419 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.79 % Allowed : 23.45 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.24), residues: 1246 helix: 0.25 (0.24), residues: 489 sheet: -0.20 (0.34), residues: 213 loop : -0.29 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 72 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.025 0.001 TYR R 148 ARG 0.018 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 109 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.4573 (mtm-85) cc_final: 0.3213 (ptt180) REVERT: A 46 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7481 (mp) REVERT: A 265 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6047 (ttt-90) REVERT: B 44 GLN cc_start: 0.6259 (mp10) cc_final: 0.5912 (mp10) REVERT: B 59 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5738 (t80) REVERT: B 142 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.5734 (m-70) REVERT: B 205 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6988 (p0) REVERT: B 217 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6095 (pmm) REVERT: B 228 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: B 261 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7737 (mp) REVERT: B 304 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6119 (mtm180) REVERT: B 325 MET cc_start: 0.5004 (mpp) cc_final: 0.4623 (ptt) REVERT: G 32 LYS cc_start: 0.6933 (mmmt) cc_final: 0.6481 (tptt) REVERT: G 59 ASN cc_start: 0.4726 (OUTLIER) cc_final: 0.4082 (t0) REVERT: N 43 LYS cc_start: 0.6225 (tmtt) cc_final: 0.5844 (mmtt) REVERT: N 46 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6601 (mm-30) REVERT: R 67 ASP cc_start: 0.6865 (p0) cc_final: 0.6551 (p0) REVERT: R 93 SER cc_start: 0.6248 (OUTLIER) cc_final: 0.6024 (p) REVERT: R 170 ARG cc_start: 0.5589 (ttt180) cc_final: 0.5327 (tpp80) REVERT: R 261 SER cc_start: 0.5508 (OUTLIER) cc_final: 0.4977 (t) REVERT: R 292 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5097 (mt-10) REVERT: R 346 LYS cc_start: 0.5686 (mttp) cc_final: 0.5399 (mtmt) REVERT: R 397 MET cc_start: 0.6418 (mmt) cc_final: 0.6216 (mmp) REVERT: R 414 ARG cc_start: 0.5581 (mmt-90) cc_final: 0.5201 (mmm160) outliers start: 41 outliers final: 24 residues processed: 137 average time/residue: 1.0377 time to fit residues: 155.9260 Evaluate side-chains 142 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 292 GLU Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN N 3 GLN R 212 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.224106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185083 restraints weight = 11178.052| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.41 r_work: 0.3989 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10352 Z= 0.139 Angle : 0.522 11.428 14044 Z= 0.270 Chirality : 0.040 0.155 1543 Planarity : 0.004 0.070 1794 Dihedral : 5.431 56.863 1419 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.79 % Allowed : 23.55 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.24), residues: 1246 helix: 0.31 (0.24), residues: 490 sheet: -0.18 (0.33), residues: 221 loop : -0.25 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.025 0.001 TYR R 148 ARG 0.018 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.10 seconds wall clock time: 67 minutes 31.67 seconds (4051.67 seconds total)