Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 03:47:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/08_2023/6x1a_21994_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/08_2023/6x1a_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_21994/08_2023/6x1a_21994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/08_2023/6x1a_21994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/08_2023/6x1a_21994_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x1a_21994/08_2023/6x1a_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-1.21rc1-5044/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: 5.55, per 1000 atoms: 0.55 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: 4.30 Conformation dependent library (CDL) restraints added in 1.5 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: 1.57 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: 2.96 Time building geometry restraints manager: 4.58 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: 5451 17.47 - 34.95: 511 34.95 - 52.42: 137 52.42 - 69.89: 27 69.89 - 87.36: 13 Dihedral angle restraints: 6139 sinusoidal: 2443 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 6136 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 6.320 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.790 ------------------------------------------------------------------------------- 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 : 15.412 87.364 3729 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 % 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 *********************** 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 : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 17 residues processed: 197 average time/residue: 1.1113 time to fit residues: 236.9976 Evaluate side-chains 139 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 2 average time/residue: 0.1143 time to fit residues: 2.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 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 187 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 268 ASN B 295 ASN B 340 ASN G 18 GLN G 24 ASN N 1 GLN N 3 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10352 Z= 0.166 Angle : 0.566 10.419 14044 Z= 0.302 Chirality : 0.041 0.158 1543 Planarity : 0.005 0.051 1794 Dihedral : 4.834 26.565 1393 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 5.45 % 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: -1.76 (0.22), residues: 1246 helix: -1.04 (0.21), residues: 494 sheet: -0.92 (0.32), residues: 221 loop : -1.23 (0.26), residues: 531 *********************** 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 185 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 126 time to evaluate : 1.151 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 31 residues processed: 178 average time/residue: 1.0400 time to fit residues: 201.5769 Evaluate side-chains 142 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.1051 time to fit residues: 2.1425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 0.0040 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 387 HIS B 110 ASN B 155 ASN B 268 ASN G 18 GLN N 1 GLN R 45 GLN R 212 HIS R 407 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10352 Z= 0.205 Angle : 0.605 11.438 14044 Z= 0.316 Chirality : 0.043 0.153 1543 Planarity : 0.005 0.057 1794 Dihedral : 5.003 25.107 1393 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 6.65 % 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: -1.20 (0.23), residues: 1246 helix: -0.57 (0.23), residues: 493 sheet: -0.52 (0.33), residues: 221 loop : -0.98 (0.27), residues: 532 *********************** 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 199 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 127 time to evaluate : 1.137 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 41 residues processed: 186 average time/residue: 0.9842 time to fit residues: 200.0915 Evaluate side-chains 157 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 36 residues processed: 5 average time/residue: 0.1318 time to fit residues: 2.6760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 1 GLN N 3 GLN N 5 GLN R 45 GLN R 212 HIS R 302 ASN R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10352 Z= 0.241 Angle : 0.632 12.358 14044 Z= 0.331 Chirality : 0.044 0.157 1543 Planarity : 0.005 0.065 1794 Dihedral : 5.237 26.412 1393 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 6.56 % 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: -1.00 (0.23), residues: 1246 helix: -0.45 (0.23), residues: 485 sheet: -0.43 (0.33), residues: 231 loop : -0.80 (0.28), residues: 530 *********************** 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 181 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 110 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 41 residues processed: 169 average time/residue: 0.9460 time to fit residues: 175.6015 Evaluate side-chains 144 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 103 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 3 average time/residue: 0.1107 time to fit residues: 2.1913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 110 ASN B 155 ASN B 268 ASN N 3 GLN N 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10352 Z= 0.162 Angle : 0.553 10.737 14044 Z= 0.290 Chirality : 0.041 0.158 1543 Planarity : 0.004 0.061 1794 Dihedral : 4.890 24.737 1393 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 6.00 % 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: -0.68 (0.24), residues: 1246 helix: -0.16 (0.23), residues: 489 sheet: -0.38 (0.33), residues: 232 loop : -0.58 (0.29), residues: 525 *********************** 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 176 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 111 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 43 residues processed: 164 average time/residue: 0.9632 time to fit residues: 173.4793 Evaluate side-chains 147 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.3715 time to fit residues: 3.8754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 187 GLN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 155 ASN N 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10352 Z= 0.152 Angle : 0.546 11.742 14044 Z= 0.285 Chirality : 0.041 0.158 1543 Planarity : 0.004 0.060 1794 Dihedral : 4.806 23.957 1393 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 5.63 % 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: -0.49 (0.24), residues: 1246 helix: 0.02 (0.24), residues: 491 sheet: -0.27 (0.33), residues: 232 loop : -0.50 (0.29), residues: 523 *********************** 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 175 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 114 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 42 residues processed: 165 average time/residue: 0.9471 time to fit residues: 171.6927 Evaluate side-chains 154 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 38 residues processed: 4 average time/residue: 0.1184 time to fit residues: 2.4224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 74 optimal weight: 0.0050 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.0600 ------------------------------------------------------------------------------- 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 279 ASN A 390 GLN B 110 ASN B 155 ASN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 10352 Z= 0.228 Angle : 0.634 13.195 14044 Z= 0.330 Chirality : 0.044 0.213 1543 Planarity : 0.005 0.062 1794 Dihedral : 5.206 38.769 1393 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 4.99 % 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: -0.57 (0.24), residues: 1246 helix: -0.12 (0.23), residues: 489 sheet: -0.26 (0.33), residues: 231 loop : -0.51 (0.29), residues: 526 *********************** 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 166 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 112 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 45 residues processed: 156 average time/residue: 0.8884 time to fit residues: 151.8475 Evaluate side-chains 157 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 6 average time/residue: 0.1318 time to fit residues: 2.8870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.0170 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 10352 Z= 0.146 Angle : 0.549 11.323 14044 Z= 0.284 Chirality : 0.041 0.159 1543 Planarity : 0.004 0.059 1794 Dihedral : 4.803 39.297 1393 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 4.62 % 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: -0.36 (0.24), residues: 1246 helix: 0.10 (0.23), residues: 491 sheet: -0.20 (0.33), residues: 227 loop : -0.42 (0.29), residues: 528 *********************** 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 162 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 112 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 37 residues processed: 156 average time/residue: 0.9415 time to fit residues: 161.7928 Evaluate side-chains 146 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 34 residues processed: 3 average time/residue: 0.1162 time to fit residues: 2.0422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 102 optimal weight: 0.0040 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 10352 Z= 0.142 Angle : 0.543 11.775 14044 Z= 0.280 Chirality : 0.040 0.156 1543 Planarity : 0.004 0.062 1794 Dihedral : 4.686 38.010 1393 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 4.25 % 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: -0.27 (0.24), residues: 1246 helix: 0.19 (0.24), residues: 491 sheet: -0.13 (0.35), residues: 212 loop : -0.38 (0.28), residues: 543 *********************** 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 160 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 114 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 37 residues processed: 154 average time/residue: 0.9695 time to fit residues: 163.7923 Evaluate side-chains 145 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 34 residues processed: 3 average time/residue: 0.1257 time to fit residues: 2.1793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 50.0000 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10352 Z= 0.148 Angle : 0.548 12.253 14044 Z= 0.282 Chirality : 0.041 0.155 1543 Planarity : 0.004 0.069 1794 Dihedral : 4.687 38.387 1393 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 3.69 % 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: -0.19 (0.24), residues: 1246 helix: 0.24 (0.24), residues: 491 sheet: -0.05 (0.34), residues: 217 loop : -0.34 (0.28), residues: 538 ********************** 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 151 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 35 residues processed: 148 average time/residue: 0.9474 time to fit residues: 154.3122 Evaluate side-chains 145 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 33 residues processed: 2 average time/residue: 0.1456 time to fit residues: 2.1290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2596 > 50: distance: 21 - 26: 21.774 distance: 26 - 27: 24.761 distance: 26 - 32: 21.432 distance: 27 - 28: 33.155 distance: 27 - 30: 31.163 distance: 28 - 29: 17.264 distance: 28 - 33: 47.868 distance: 30 - 31: 14.456 distance: 31 - 32: 8.289 distance: 33 - 34: 38.420 distance: 34 - 35: 42.050 distance: 34 - 37: 42.250 distance: 35 - 36: 8.569 distance: 35 - 42: 8.671 distance: 37 - 38: 38.937 distance: 38 - 39: 35.635 distance: 39 - 40: 5.879 distance: 39 - 41: 21.158 distance: 42 - 43: 7.952 distance: 43 - 44: 19.517 distance: 43 - 46: 24.758 distance: 44 - 45: 20.582 distance: 44 - 53: 11.348 distance: 46 - 47: 11.131 distance: 47 - 48: 27.835 distance: 47 - 49: 20.037 distance: 48 - 50: 12.265 distance: 49 - 51: 9.107 distance: 50 - 52: 31.122 distance: 51 - 52: 8.605 distance: 53 - 54: 41.396 distance: 54 - 55: 40.339 distance: 54 - 57: 19.606 distance: 55 - 56: 11.640 distance: 55 - 58: 10.215 distance: 58 - 59: 17.615 distance: 59 - 60: 14.834 distance: 59 - 62: 36.158 distance: 60 - 61: 11.674 distance: 60 - 69: 4.098 distance: 62 - 63: 7.673 distance: 63 - 64: 10.974 distance: 64 - 65: 5.339 distance: 65 - 66: 10.686 distance: 66 - 67: 12.361 distance: 66 - 68: 20.435 distance: 69 - 70: 4.204 distance: 70 - 71: 14.681 distance: 70 - 73: 5.682 distance: 71 - 72: 9.532 distance: 71 - 81: 8.164 distance: 73 - 74: 4.634 distance: 74 - 75: 4.380 distance: 74 - 76: 7.072 distance: 75 - 77: 3.525 distance: 76 - 78: 6.132 distance: 77 - 79: 6.908 distance: 78 - 79: 8.468 distance: 79 - 80: 5.498 distance: 81 - 82: 17.328 distance: 82 - 83: 13.432 distance: 82 - 85: 10.625 distance: 83 - 84: 19.435 distance: 83 - 88: 10.640 distance: 85 - 86: 7.281 distance: 85 - 87: 20.206 distance: 88 - 89: 22.515 distance: 89 - 90: 15.580 distance: 89 - 92: 12.712 distance: 90 - 91: 11.015 distance: 90 - 95: 18.953 distance: 92 - 93: 19.135 distance: 92 - 94: 17.976 distance: 95 - 96: 10.638 distance: 95 - 101: 12.185 distance: 96 - 97: 16.295 distance: 96 - 99: 31.449 distance: 97 - 98: 30.639 distance: 97 - 102: 13.035 distance: 99 - 100: 11.066 distance: 100 - 101: 21.375 distance: 102 - 103: 30.978 distance: 103 - 104: 8.218 distance: 103 - 106: 22.210 distance: 104 - 111: 30.571 distance: 106 - 107: 17.372 distance: 108 - 109: 17.787