Starting phenix.real_space_refine on Thu Sep 18 13:01:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j35_61106/09_2025/9j35_61106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j35_61106/09_2025/9j35_61106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j35_61106/09_2025/9j35_61106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j35_61106/09_2025/9j35_61106.map" model { file = "/net/cci-nas-00/data/ceres_data/9j35_61106/09_2025/9j35_61106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j35_61106/09_2025/9j35_61106.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 11008 2.51 5 N 2840 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16960 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "B" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "C" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Time building chain proxies: 4.04, per 1000 atoms: 0.24 Number of scatterers: 16960 At special positions: 0 Unit cell: (109.044, 110.908, 139.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3012 8.00 N 2840 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 310 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 303 " distance=1.34 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 310 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 310 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 297 " - pdb=" SG CYS C 303 " distance=1.34 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 292 " - pdb=" SG CYS D 333 " distance=2.04 Simple disulfide: pdb=" SG CYS D 297 " - pdb=" SG CYS D 303 " distance=1.46 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 766.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 16 sheets defined 57.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.637A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.561A pdb=" N PHE A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 159 removed outlier: 3.776A pdb=" N ALA A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.094A pdb=" N ALA A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.679A pdb=" N TRP A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.914A pdb=" N TYR A 270 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 removed outlier: 3.516A pdb=" N TRP A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.758A pdb=" N VAL A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.518A pdb=" N LEU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 removed outlier: 3.657A pdb=" N LYS A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 421 removed outlier: 3.514A pdb=" N ILE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 444 removed outlier: 3.642A pdb=" N GLU A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 465 removed outlier: 3.895A pdb=" N GLU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.561A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 491 " --> pdb=" O HIS A 487 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 493 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.951A pdb=" N SER A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.709A pdb=" N ILE A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 removed outlier: 3.921A pdb=" N THR A 573 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 4.395A pdb=" N PHE A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.671A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 removed outlier: 3.713A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.536A pdb=" N PHE B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.725A pdb=" N ALA B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.568A pdb=" N TRP B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.554A pdb=" N VAL B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.743A pdb=" N PHE B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.575A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 294 removed outlier: 3.694A pdb=" N TYR B 270 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.590A pdb=" N TRP B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 removed outlier: 3.790A pdb=" N VAL B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.515A pdb=" N LEU B 353 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 380 removed outlier: 3.657A pdb=" N LYS B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 370 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 421 removed outlier: 3.523A pdb=" N PHE B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 444 removed outlier: 3.640A pdb=" N GLU B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 465 removed outlier: 3.895A pdb=" N GLU B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 452 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.550A pdb=" N ASP B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 491 " --> pdb=" O HIS B 487 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.967A pdb=" N SER B 501 " --> pdb=" O PRO B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.765A pdb=" N THR B 573 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 4.439A pdb=" N PHE B 609 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 104 through 111 removed outlier: 3.630A pdb=" N LEU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 119 removed outlier: 3.578A pdb=" N PHE C 117 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 144 removed outlier: 3.726A pdb=" N ALA C 137 " --> pdb=" O ASP C 133 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 179 through 191 removed outlier: 4.311A pdb=" N ALA C 184 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 186 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.839A pdb=" N ILE C 205 " --> pdb=" O PRO C 201 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.572A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 294 removed outlier: 3.756A pdb=" N TYR C 270 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS C 275 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.533A pdb=" N TRP C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.788A pdb=" N VAL C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.521A pdb=" N LEU C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 380 removed outlier: 3.658A pdb=" N LYS C 366 " --> pdb=" O ASN C 362 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 370 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 423 removed outlier: 3.755A pdb=" N LEU C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 444 removed outlier: 3.649A pdb=" N GLU C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 465 removed outlier: 3.714A pdb=" N ARG C 452 " --> pdb=" O ASP C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 Processing helix chain 'C' and resid 477 through 494 removed outlier: 6.122A pdb=" N ALA C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 493 " --> pdb=" O CYS C 489 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 569 through 576 removed outlier: 3.963A pdb=" N THR C 573 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 4.464A pdb=" N PHE C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.902A pdb=" N TYR D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 3.604A pdb=" N LEU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.574A pdb=" N PHE D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.752A pdb=" N ALA D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.842A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.795A pdb=" N LEU D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.774A pdb=" N TRP D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.698A pdb=" N SER D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 294 removed outlier: 3.915A pdb=" N TYR D 270 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.536A pdb=" N TRP D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.921A pdb=" N VAL D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.517A pdb=" N LEU D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 379 removed outlier: 3.652A pdb=" N LYS D 366 " --> pdb=" O ASN D 362 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 370 " --> pdb=" O LYS D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 421 removed outlier: 3.528A pdb=" N LEU D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 421 " --> pdb=" O THR D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 446 through 465 removed outlier: 3.870A pdb=" N GLU D 451 " --> pdb=" O GLN D 447 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 452 " --> pdb=" O ASP D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 474 Processing helix chain 'D' and resid 477 through 494 removed outlier: 3.518A pdb=" N ARG D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS D 487 " --> pdb=" O ASP D 483 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 488 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 490 " --> pdb=" O ARG D 486 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 491 " --> pdb=" O HIS D 487 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 493 " --> pdb=" O CYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 577 removed outlier: 3.921A pdb=" N THR D 573 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 612 removed outlier: 4.395A pdb=" N PHE D 609 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 610 " --> pdb=" O GLU D 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.647A pdb=" N TYR A 163 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 519 removed outlier: 6.598A pdb=" N GLU A 598 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.648A pdb=" N VAL A 591 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 124 Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.684A pdb=" N TYR B 163 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 515 through 519 removed outlier: 6.588A pdb=" N GLU B 598 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.649A pdb=" N VAL B 591 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=AB1, first strand: chain 'C' and resid 163 through 165 Processing sheet with id=AB2, first strand: chain 'C' and resid 515 through 519 removed outlier: 6.586A pdb=" N GLU C 598 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.574A pdb=" N VAL C 591 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 561 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 121 through 124 Processing sheet with id=AB5, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.773A pdb=" N TYR D 163 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 515 through 519 removed outlier: 6.597A pdb=" N GLU D 598 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.648A pdb=" N VAL D 591 " --> pdb=" O LEU D 525 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1944 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: 2.65 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2703 1.28 - 1.42: 4617 1.42 - 1.55: 9867 1.55 - 1.69: 17 1.69 - 1.82: 144 Bond restraints: 17348 Sorted by residual: bond pdb=" C LEU A 411 " pdb=" N ILE A 412 " ideal model delta sigma weight residual 1.335 1.588 -0.253 1.20e-02 6.94e+03 4.45e+02 bond pdb=" N PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.473 1.227 0.246 1.40e-02 5.10e+03 3.08e+02 bond pdb=" C LEU B 411 " pdb=" N ILE B 412 " ideal model delta sigma weight residual 1.335 1.541 -0.206 1.20e-02 6.94e+03 2.94e+02 bond pdb=" C LEU B 378 " pdb=" N SER B 379 " ideal model delta sigma weight residual 1.334 1.566 -0.232 1.49e-02 4.50e+03 2.43e+02 bond pdb=" C MET D 512 " pdb=" N ARG D 513 " ideal model delta sigma weight residual 1.333 1.567 -0.234 1.51e-02 4.39e+03 2.40e+02 ... (remaining 17343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 23306 5.50 - 11.01: 186 11.01 - 16.51: 9 16.51 - 22.02: 4 22.02 - 27.52: 3 Bond angle restraints: 23508 Sorted by residual: angle pdb=" CA LEU D 378 " pdb=" C LEU D 378 " pdb=" N SER D 379 " ideal model delta sigma weight residual 118.14 142.73 -24.59 1.31e+00 5.83e-01 3.52e+02 angle pdb=" O LEU D 378 " pdb=" C LEU D 378 " pdb=" N SER D 379 " ideal model delta sigma weight residual 122.43 97.37 25.06 1.34e+00 5.57e-01 3.50e+02 angle pdb=" C LEU D 378 " pdb=" N SER D 379 " pdb=" CA SER D 379 " ideal model delta sigma weight residual 121.66 149.18 -27.52 1.76e+00 3.23e-01 2.44e+02 angle pdb=" O LEU B 378 " pdb=" C LEU B 378 " pdb=" N SER B 379 " ideal model delta sigma weight residual 122.27 103.72 18.55 1.23e+00 6.61e-01 2.28e+02 angle pdb=" CA LEU B 378 " pdb=" C LEU B 378 " pdb=" N SER B 379 " ideal model delta sigma weight residual 117.72 136.95 -19.23 1.31e+00 5.83e-01 2.16e+02 ... (remaining 23503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 9217 17.87 - 35.74: 966 35.74 - 53.61: 180 53.61 - 71.48: 35 71.48 - 89.35: 10 Dihedral angle restraints: 10408 sinusoidal: 4240 harmonic: 6168 Sorted by residual: dihedral pdb=" C TYR B 234 " pdb=" N TYR B 234 " pdb=" CA TYR B 234 " pdb=" CB TYR B 234 " ideal model delta harmonic sigma weight residual -122.60 -102.43 -20.17 0 2.50e+00 1.60e-01 6.51e+01 dihedral pdb=" C GLN B 233 " pdb=" N GLN B 233 " pdb=" CA GLN B 233 " pdb=" CB GLN B 233 " ideal model delta harmonic sigma weight residual -122.60 -105.50 -17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" CA ASP B 148 " pdb=" C ASP B 148 " pdb=" N VAL B 149 " pdb=" CA VAL B 149 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 10405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2201 0.084 - 0.167: 393 0.167 - 0.251: 39 0.251 - 0.335: 13 0.335 - 0.419: 6 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CA SER A 379 " pdb=" N SER A 379 " pdb=" C SER A 379 " pdb=" CB SER A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA LEU C 381 " pdb=" N LEU C 381 " pdb=" C LEU C 381 " pdb=" CB LEU C 381 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA SER C 379 " pdb=" N SER C 379 " pdb=" C SER C 379 " pdb=" CB SER C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2649 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 201 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C PRO B 201 " -0.088 2.00e-02 2.50e+03 pdb=" O PRO B 201 " 0.033 2.00e-02 2.50e+03 pdb=" N LEU B 202 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 414 " 0.027 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ASN D 414 " -0.087 2.00e-02 2.50e+03 pdb=" O ASN D 414 " 0.030 2.00e-02 2.50e+03 pdb=" N MET D 415 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 235 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 236 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.057 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 574 2.71 - 3.26: 14752 3.26 - 3.80: 24301 3.80 - 4.35: 32427 4.35 - 4.90: 54291 Nonbonded interactions: 126345 Sorted by model distance: nonbonded pdb=" O LEU B 200 " pdb=" NE2 GLN B 233 " model vdw 2.161 3.120 nonbonded pdb=" O ALA D 509 " pdb=" NH1 ARG D 513 " model vdw 2.243 3.120 nonbonded pdb=" OG SER B 167 " pdb=" O SER B 168 " model vdw 2.282 3.040 nonbonded pdb=" O GLN C 383 " pdb=" CG GLN C 383 " model vdw 2.312 3.440 nonbonded pdb=" O SER B 522 " pdb=" OG SER B 522 " model vdw 2.314 3.040 ... (remaining 126340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.200 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.014 0.688 17360 Z= 0.782 Angle : 1.442 41.918 23532 Z= 0.866 Chirality : 0.069 0.419 2652 Planarity : 0.008 0.104 2948 Dihedral : 15.060 89.353 6372 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 0.76 % Allowed : 5.62 % Favored : 93.63 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.07 (0.13), residues: 2076 helix: -3.36 (0.11), residues: 1236 sheet: -2.45 (0.32), residues: 160 loop : -3.14 (0.17), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 169 TYR 0.033 0.004 TYR D 234 PHE 0.023 0.003 PHE B 171 TRP 0.019 0.004 TRP C 373 HIS 0.012 0.003 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.01163 (17348) covalent geometry : angle 1.37119 (23508) SS BOND : bond 0.32529 ( 12) SS BOND : angle 14.00219 ( 24) hydrogen bonds : bond 0.28151 ( 691) hydrogen bonds : angle 7.90873 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.699 Fit side-chains REVERT: A 112 PHE cc_start: 0.7858 (m-80) cc_final: 0.7248 (t80) REVERT: B 112 PHE cc_start: 0.7919 (m-80) cc_final: 0.7325 (t80) REVERT: B 265 TYR cc_start: 0.8322 (t80) cc_final: 0.8106 (t80) REVERT: C 246 SER cc_start: 0.7714 (m) cc_final: 0.7345 (p) REVERT: C 444 MET cc_start: 0.8200 (mmt) cc_final: 0.7783 (mmt) REVERT: D 334 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7971 (ptt-90) REVERT: D 415 MET cc_start: 0.8112 (tpp) cc_final: 0.7696 (tpp) outliers start: 14 outliers final: 4 residues processed: 240 average time/residue: 0.7584 time to fit residues: 198.7167 Evaluate side-chains 178 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain D residue 234 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 322 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.194423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130588 restraints weight = 17633.341| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.92 r_work: 0.3256 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17360 Z= 0.137 Angle : 0.633 8.197 23532 Z= 0.335 Chirality : 0.041 0.141 2652 Planarity : 0.005 0.065 2948 Dihedral : 6.051 55.894 2316 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.62 % Allowed : 11.29 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.16), residues: 2076 helix: -1.80 (0.14), residues: 1232 sheet: -2.01 (0.31), residues: 180 loop : -2.71 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 540 TYR 0.018 0.001 TYR C 187 PHE 0.016 0.001 PHE D 255 TRP 0.016 0.001 TRP B 281 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00281 (17348) covalent geometry : angle 0.63119 (23508) SS BOND : bond 0.00346 ( 12) SS BOND : angle 1.69492 ( 24) hydrogen bonds : bond 0.07143 ( 691) hydrogen bonds : angle 4.60192 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7830 (m-80) cc_final: 0.6929 (t80) REVERT: A 287 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: A 415 MET cc_start: 0.8831 (tpp) cc_final: 0.8429 (tpp) REVERT: A 427 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8940 (mm-30) REVERT: B 112 PHE cc_start: 0.7845 (m-80) cc_final: 0.6982 (t80) REVERT: B 155 MET cc_start: 0.6270 (tmm) cc_final: 0.5400 (tmm) REVERT: B 287 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: C 155 MET cc_start: 0.6613 (tpp) cc_final: 0.6309 (tpp) REVERT: C 287 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: C 444 MET cc_start: 0.8622 (mmt) cc_final: 0.8350 (mmt) REVERT: D 108 ILE cc_start: 0.8534 (mt) cc_final: 0.8322 (mm) REVERT: D 235 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7423 (mp) REVERT: D 249 LYS cc_start: 0.6175 (tppt) cc_final: 0.5462 (tppt) REVERT: D 287 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: D 334 ARG cc_start: 0.8515 (ptt-90) cc_final: 0.8219 (ptt-90) REVERT: D 381 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 415 MET cc_start: 0.8797 (tpp) cc_final: 0.8521 (tpp) outliers start: 30 outliers final: 9 residues processed: 230 average time/residue: 0.6987 time to fit residues: 177.0062 Evaluate side-chains 202 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 381 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.196646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137542 restraints weight = 17769.867| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.18 r_work: 0.3262 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17360 Z= 0.107 Angle : 0.553 9.040 23532 Z= 0.290 Chirality : 0.039 0.135 2652 Planarity : 0.004 0.053 2948 Dihedral : 5.529 57.971 2316 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.94 % Allowed : 13.44 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.18), residues: 2076 helix: -0.78 (0.16), residues: 1164 sheet: -1.05 (0.32), residues: 220 loop : -2.42 (0.18), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 540 TYR 0.015 0.001 TYR C 187 PHE 0.025 0.001 PHE A 150 TRP 0.014 0.001 TRP B 281 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00216 (17348) covalent geometry : angle 0.54945 (23508) SS BOND : bond 0.00284 ( 12) SS BOND : angle 2.02380 ( 24) hydrogen bonds : bond 0.05756 ( 691) hydrogen bonds : angle 4.12460 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7648 (mm) cc_final: 0.7410 (mm) REVERT: A 112 PHE cc_start: 0.7854 (m-80) cc_final: 0.6915 (t80) REVERT: A 415 MET cc_start: 0.8859 (tpp) cc_final: 0.8509 (tpp) REVERT: A 429 MET cc_start: 0.9116 (tmm) cc_final: 0.8907 (ttp) REVERT: A 440 MET cc_start: 0.8794 (mtm) cc_final: 0.8580 (mtm) REVERT: A 512 MET cc_start: 0.7894 (mmm) cc_final: 0.7642 (mmt) REVERT: A 533 ASP cc_start: 0.8585 (t0) cc_final: 0.8102 (t0) REVERT: B 112 PHE cc_start: 0.7857 (m-80) cc_final: 0.6977 (t80) REVERT: B 155 MET cc_start: 0.6096 (tmm) cc_final: 0.5247 (mtm) REVERT: B 415 MET cc_start: 0.8695 (tpp) cc_final: 0.8427 (tpp) REVERT: B 428 GLU cc_start: 0.8916 (tt0) cc_final: 0.8519 (mt-10) REVERT: B 533 ASP cc_start: 0.8597 (t0) cc_final: 0.8104 (t0) REVERT: C 155 MET cc_start: 0.6607 (tpp) cc_final: 0.6151 (tpp) REVERT: D 108 ILE cc_start: 0.8447 (mt) cc_final: 0.8225 (mm) REVERT: D 199 VAL cc_start: 0.6801 (OUTLIER) cc_final: 0.6107 (m) REVERT: D 249 LYS cc_start: 0.5799 (tppt) cc_final: 0.5032 (tppt) REVERT: D 334 ARG cc_start: 0.8517 (ptt-90) cc_final: 0.8125 (ptt-90) REVERT: D 381 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 415 MET cc_start: 0.8746 (tpp) cc_final: 0.8504 (tpp) outliers start: 36 outliers final: 15 residues processed: 213 average time/residue: 0.6861 time to fit residues: 160.4153 Evaluate side-chains 199 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 0.0030 chunk 87 optimal weight: 0.0470 chunk 110 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.1888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.202251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143822 restraints weight = 17994.785| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.90 r_work: 0.3418 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17360 Z= 0.089 Angle : 0.495 9.812 23532 Z= 0.258 Chirality : 0.038 0.162 2652 Planarity : 0.003 0.051 2948 Dihedral : 5.107 59.635 2316 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.84 % Allowed : 14.15 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.18), residues: 2076 helix: -0.19 (0.17), residues: 1168 sheet: -0.59 (0.33), residues: 220 loop : -2.37 (0.18), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 540 TYR 0.015 0.001 TYR C 187 PHE 0.009 0.001 PHE D 255 TRP 0.012 0.001 TRP B 281 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00170 (17348) covalent geometry : angle 0.49261 (23508) SS BOND : bond 0.00845 ( 12) SS BOND : angle 1.48291 ( 24) hydrogen bonds : bond 0.04026 ( 691) hydrogen bonds : angle 3.82564 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7842 (m-80) cc_final: 0.6908 (t80) REVERT: A 199 VAL cc_start: 0.6718 (OUTLIER) cc_final: 0.6347 (m) REVERT: A 415 MET cc_start: 0.8796 (tpp) cc_final: 0.8494 (tpp) REVERT: A 429 MET cc_start: 0.9022 (tmm) cc_final: 0.8810 (ttp) REVERT: A 533 ASP cc_start: 0.8591 (t0) cc_final: 0.8164 (t0) REVERT: B 112 PHE cc_start: 0.7831 (m-80) cc_final: 0.7008 (t80) REVERT: B 155 MET cc_start: 0.6106 (tmm) cc_final: 0.5317 (mtm) REVERT: B 287 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 504 ASP cc_start: 0.7095 (t0) cc_final: 0.6723 (t0) REVERT: B 533 ASP cc_start: 0.8609 (t0) cc_final: 0.8187 (t0) REVERT: C 155 MET cc_start: 0.6830 (tpp) cc_final: 0.6221 (tpp) REVERT: C 199 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6545 (m) REVERT: D 199 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6290 (m) REVERT: D 249 LYS cc_start: 0.5865 (tppt) cc_final: 0.5060 (tppt) REVERT: D 334 ARG cc_start: 0.8581 (ptt-90) cc_final: 0.8206 (ptt-90) REVERT: D 424 ILE cc_start: 0.8042 (tt) cc_final: 0.7789 (pt) outliers start: 34 outliers final: 15 residues processed: 229 average time/residue: 0.6161 time to fit residues: 155.2782 Evaluate side-chains 210 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 148 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 181 optimal weight: 0.3980 chunk 151 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 275 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134204 restraints weight = 17614.536| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.01 r_work: 0.3260 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17360 Z= 0.172 Angle : 0.631 10.126 23532 Z= 0.327 Chirality : 0.043 0.148 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.529 59.445 2316 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.97 % Allowed : 15.06 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.18), residues: 2076 helix: -0.47 (0.16), residues: 1192 sheet: -0.46 (0.33), residues: 220 loop : -2.41 (0.19), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 558 TYR 0.014 0.002 TYR C 270 PHE 0.028 0.002 PHE A 150 TRP 0.011 0.002 TRP C 574 HIS 0.008 0.002 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00401 (17348) covalent geometry : angle 0.62762 (23508) SS BOND : bond 0.00639 ( 12) SS BOND : angle 2.21097 ( 24) hydrogen bonds : bond 0.08170 ( 691) hydrogen bonds : angle 4.14286 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7757 (m-80) cc_final: 0.6824 (t80) REVERT: A 199 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6421 (m) REVERT: A 415 MET cc_start: 0.8687 (tpp) cc_final: 0.8409 (tpp) REVERT: A 428 GLU cc_start: 0.8866 (tt0) cc_final: 0.8645 (mt-10) REVERT: A 533 ASP cc_start: 0.8569 (t0) cc_final: 0.8080 (t0) REVERT: B 112 PHE cc_start: 0.7730 (m-80) cc_final: 0.6799 (t80) REVERT: B 155 MET cc_start: 0.6093 (tmm) cc_final: 0.5090 (mtm) REVERT: B 323 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7487 (mmp80) REVERT: B 428 GLU cc_start: 0.8841 (tt0) cc_final: 0.8398 (mt-10) REVERT: B 504 ASP cc_start: 0.7177 (t0) cc_final: 0.6795 (t0) REVERT: B 533 ASP cc_start: 0.8563 (t0) cc_final: 0.8093 (t0) REVERT: C 155 MET cc_start: 0.6710 (tpp) cc_final: 0.6279 (tpp) REVERT: C 400 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8867 (mt) REVERT: C 506 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7921 (pp) REVERT: C 530 ASP cc_start: 0.8029 (m-30) cc_final: 0.7827 (m-30) REVERT: D 171 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.4142 (p90) REVERT: D 249 LYS cc_start: 0.5913 (tppt) cc_final: 0.5163 (tppt) REVERT: D 334 ARG cc_start: 0.8423 (ptt-90) cc_final: 0.8028 (ptt-90) REVERT: D 381 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 495 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.7087 (mmm-85) outliers start: 55 outliers final: 34 residues processed: 227 average time/residue: 0.6622 time to fit residues: 166.5608 Evaluate side-chains 217 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 HIS C 383 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.192312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131475 restraints weight = 17508.832| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.22 r_work: 0.3138 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17360 Z= 0.173 Angle : 0.634 10.958 23532 Z= 0.330 Chirality : 0.043 0.146 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.610 59.437 2316 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.97 % Allowed : 15.82 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.18), residues: 2076 helix: -0.50 (0.16), residues: 1192 sheet: -0.34 (0.33), residues: 220 loop : -2.43 (0.19), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 558 TYR 0.014 0.002 TYR B 151 PHE 0.016 0.002 PHE B 171 TRP 0.013 0.002 TRP C 574 HIS 0.008 0.002 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00402 (17348) covalent geometry : angle 0.63063 (23508) SS BOND : bond 0.00420 ( 12) SS BOND : angle 2.04251 ( 24) hydrogen bonds : bond 0.08010 ( 691) hydrogen bonds : angle 4.14759 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7798 (m-80) cc_final: 0.6951 (t80) REVERT: A 199 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6445 (m) REVERT: A 415 MET cc_start: 0.8718 (tpp) cc_final: 0.8449 (tpp) REVERT: A 504 ASP cc_start: 0.7140 (t0) cc_final: 0.6814 (t0) REVERT: A 533 ASP cc_start: 0.8599 (t0) cc_final: 0.8089 (t0) REVERT: B 112 PHE cc_start: 0.7748 (m-80) cc_final: 0.6930 (t80) REVERT: B 155 MET cc_start: 0.6129 (tmm) cc_final: 0.5146 (mtm) REVERT: B 323 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7506 (mmp80) REVERT: B 504 ASP cc_start: 0.7161 (t0) cc_final: 0.6758 (t0) REVERT: B 533 ASP cc_start: 0.8580 (t0) cc_final: 0.8071 (t0) REVERT: C 155 MET cc_start: 0.6834 (tpp) cc_final: 0.6464 (tpp) REVERT: C 199 VAL cc_start: 0.7026 (OUTLIER) cc_final: 0.6533 (m) REVERT: C 381 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8493 (mp) REVERT: C 400 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8891 (mt) REVERT: D 171 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.4268 (p90) REVERT: D 249 LYS cc_start: 0.5966 (tppt) cc_final: 0.5215 (tppt) REVERT: D 334 ARG cc_start: 0.8458 (ptt-90) cc_final: 0.8053 (ptt-90) REVERT: D 381 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8529 (mp) outliers start: 55 outliers final: 35 residues processed: 231 average time/residue: 0.6240 time to fit residues: 159.5831 Evaluate side-chains 226 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.192562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128413 restraints weight = 17397.405| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.97 r_work: 0.3200 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17360 Z= 0.160 Angle : 0.620 13.116 23532 Z= 0.320 Chirality : 0.042 0.175 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.551 58.622 2316 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.75 % Allowed : 16.58 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.18), residues: 2076 helix: -0.42 (0.16), residues: 1192 sheet: -0.22 (0.33), residues: 220 loop : -2.42 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 558 TYR 0.013 0.002 TYR B 151 PHE 0.031 0.001 PHE C 150 TRP 0.017 0.002 TRP C 574 HIS 0.008 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00366 (17348) covalent geometry : angle 0.61695 (23508) SS BOND : bond 0.00411 ( 12) SS BOND : angle 1.89873 ( 24) hydrogen bonds : bond 0.07719 ( 691) hydrogen bonds : angle 4.10412 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7851 (m-80) cc_final: 0.6941 (t80) REVERT: A 199 VAL cc_start: 0.6880 (OUTLIER) cc_final: 0.6434 (m) REVERT: A 415 MET cc_start: 0.8802 (tpp) cc_final: 0.8553 (tpp) REVERT: A 504 ASP cc_start: 0.7228 (t0) cc_final: 0.6905 (t0) REVERT: A 533 ASP cc_start: 0.8622 (t0) cc_final: 0.8104 (t0) REVERT: B 112 PHE cc_start: 0.7853 (m-80) cc_final: 0.6981 (t80) REVERT: B 155 MET cc_start: 0.6151 (tmm) cc_final: 0.5177 (mtm) REVERT: B 323 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7519 (mmp80) REVERT: B 504 ASP cc_start: 0.7226 (t0) cc_final: 0.6804 (t0) REVERT: B 533 ASP cc_start: 0.8615 (t0) cc_final: 0.8100 (t0) REVERT: C 108 ILE cc_start: 0.8522 (mp) cc_final: 0.8182 (mp) REVERT: C 155 MET cc_start: 0.6870 (tpp) cc_final: 0.6466 (tpp) REVERT: C 199 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6548 (m) REVERT: C 381 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 400 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8881 (mt) REVERT: D 171 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.4254 (p90) REVERT: D 249 LYS cc_start: 0.5769 (tppt) cc_final: 0.5027 (tppt) REVERT: D 334 ARG cc_start: 0.8477 (ptt-90) cc_final: 0.8098 (ptt-90) outliers start: 51 outliers final: 36 residues processed: 226 average time/residue: 0.6386 time to fit residues: 160.3587 Evaluate side-chains 224 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 164 optimal weight: 0.0010 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.1980 chunk 204 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 163 optimal weight: 7.9990 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.198000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134954 restraints weight = 17671.538| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.94 r_work: 0.3293 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17360 Z= 0.095 Angle : 0.517 12.814 23532 Z= 0.267 Chirality : 0.038 0.155 2652 Planarity : 0.003 0.051 2948 Dihedral : 5.135 58.616 2316 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.67 % Allowed : 17.87 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.19), residues: 2076 helix: 0.20 (0.17), residues: 1156 sheet: -0.22 (0.33), residues: 228 loop : -2.30 (0.19), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 540 TYR 0.013 0.001 TYR C 187 PHE 0.015 0.001 PHE C 566 TRP 0.019 0.001 TRP C 574 HIS 0.005 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00185 (17348) covalent geometry : angle 0.51546 (23508) SS BOND : bond 0.00320 ( 12) SS BOND : angle 1.47381 ( 24) hydrogen bonds : bond 0.04867 ( 691) hydrogen bonds : angle 3.79237 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7801 (m-80) cc_final: 0.6858 (t80) REVERT: A 199 VAL cc_start: 0.6800 (OUTLIER) cc_final: 0.6379 (m) REVERT: A 504 ASP cc_start: 0.7225 (t0) cc_final: 0.6884 (t0) REVERT: A 533 ASP cc_start: 0.8604 (t0) cc_final: 0.8112 (t0) REVERT: B 112 PHE cc_start: 0.7819 (m-80) cc_final: 0.6955 (t80) REVERT: B 155 MET cc_start: 0.6036 (tmm) cc_final: 0.5077 (mtm) REVERT: B 323 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7469 (mmp80) REVERT: B 415 MET cc_start: 0.8565 (tpp) cc_final: 0.8263 (tpp) REVERT: B 504 ASP cc_start: 0.6996 (t0) cc_final: 0.6611 (t0) REVERT: B 533 ASP cc_start: 0.8602 (t0) cc_final: 0.8149 (t0) REVERT: B 569 GLU cc_start: 0.8223 (pm20) cc_final: 0.8002 (pm20) REVERT: C 108 ILE cc_start: 0.8362 (mp) cc_final: 0.8024 (mp) REVERT: C 155 MET cc_start: 0.6933 (tpp) cc_final: 0.6601 (tpp) REVERT: C 199 VAL cc_start: 0.6940 (OUTLIER) cc_final: 0.6514 (m) REVERT: C 226 LEU cc_start: 0.6987 (mt) cc_final: 0.6688 (mt) REVERT: C 244 LEU cc_start: 0.7298 (mp) cc_final: 0.6579 (tp) REVERT: D 249 LYS cc_start: 0.5788 (tppt) cc_final: 0.5024 (tppt) REVERT: D 334 ARG cc_start: 0.8505 (ptt-90) cc_final: 0.8121 (ptt-90) REVERT: D 565 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7916 (mt-10) outliers start: 31 outliers final: 19 residues processed: 216 average time/residue: 0.6925 time to fit residues: 165.4671 Evaluate side-chains 203 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 565 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.193589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136900 restraints weight = 17551.565| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.82 r_work: 0.3271 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17360 Z= 0.149 Angle : 0.600 13.718 23532 Z= 0.308 Chirality : 0.042 0.173 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.348 58.696 2316 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.67 % Allowed : 18.30 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 2076 helix: -0.06 (0.16), residues: 1176 sheet: -0.22 (0.33), residues: 228 loop : -2.32 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 540 TYR 0.013 0.002 TYR C 270 PHE 0.031 0.001 PHE C 150 TRP 0.023 0.002 TRP C 574 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00339 (17348) covalent geometry : angle 0.59744 (23508) SS BOND : bond 0.00449 ( 12) SS BOND : angle 1.95473 ( 24) hydrogen bonds : bond 0.07333 ( 691) hydrogen bonds : angle 3.99060 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7726 (m-80) cc_final: 0.6709 (t80) REVERT: A 199 VAL cc_start: 0.6759 (OUTLIER) cc_final: 0.6317 (m) REVERT: A 504 ASP cc_start: 0.7158 (t0) cc_final: 0.6814 (t0) REVERT: A 533 ASP cc_start: 0.8601 (t0) cc_final: 0.8071 (t0) REVERT: B 112 PHE cc_start: 0.7688 (m-80) cc_final: 0.6696 (t80) REVERT: B 155 MET cc_start: 0.5938 (tmm) cc_final: 0.4983 (mtm) REVERT: B 323 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7411 (mmp80) REVERT: B 504 ASP cc_start: 0.7124 (t0) cc_final: 0.6719 (t0) REVERT: B 533 ASP cc_start: 0.8598 (t0) cc_final: 0.8088 (t0) REVERT: B 569 GLU cc_start: 0.8155 (pm20) cc_final: 0.7929 (pm20) REVERT: C 155 MET cc_start: 0.6830 (tpp) cc_final: 0.6488 (tpp) REVERT: C 199 VAL cc_start: 0.6986 (OUTLIER) cc_final: 0.6482 (m) REVERT: C 204 GLN cc_start: 0.5788 (OUTLIER) cc_final: 0.5431 (mp10) REVERT: C 226 LEU cc_start: 0.6815 (mt) cc_final: 0.6521 (mt) REVERT: C 244 LEU cc_start: 0.7134 (mp) cc_final: 0.6405 (tp) REVERT: D 171 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.4007 (p90) REVERT: D 249 LYS cc_start: 0.5675 (tppt) cc_final: 0.4947 (tppt) REVERT: D 334 ARG cc_start: 0.8386 (ptt-90) cc_final: 0.7965 (ptt-90) REVERT: D 381 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8463 (mp) outliers start: 31 outliers final: 19 residues processed: 210 average time/residue: 0.6876 time to fit residues: 159.2050 Evaluate side-chains 203 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 32 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 160 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 202 optimal weight: 0.3980 chunk 185 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135034 restraints weight = 17475.158| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.13 r_work: 0.3221 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17360 Z= 0.112 Angle : 0.553 13.822 23532 Z= 0.283 Chirality : 0.040 0.169 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.174 58.103 2316 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.40 % Allowed : 18.63 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.18), residues: 2076 helix: 0.22 (0.17), residues: 1160 sheet: -0.12 (0.33), residues: 228 loop : -2.29 (0.19), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 540 TYR 0.012 0.001 TYR C 187 PHE 0.014 0.001 PHE C 566 TRP 0.026 0.001 TRP C 574 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00234 (17348) covalent geometry : angle 0.55010 (23508) SS BOND : bond 0.00332 ( 12) SS BOND : angle 1.71909 ( 24) hydrogen bonds : bond 0.05919 ( 691) hydrogen bonds : angle 3.89273 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7847 (m-80) cc_final: 0.6906 (t80) REVERT: A 199 VAL cc_start: 0.6731 (OUTLIER) cc_final: 0.6308 (m) REVERT: A 504 ASP cc_start: 0.7234 (t0) cc_final: 0.6876 (t0) REVERT: A 533 ASP cc_start: 0.8666 (t0) cc_final: 0.8153 (t0) REVERT: B 112 PHE cc_start: 0.7848 (m-80) cc_final: 0.6978 (t80) REVERT: B 155 MET cc_start: 0.6023 (tmm) cc_final: 0.5029 (mtm) REVERT: B 323 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7497 (mmp80) REVERT: B 504 ASP cc_start: 0.7033 (t0) cc_final: 0.6666 (t0) REVERT: B 533 ASP cc_start: 0.8622 (t0) cc_final: 0.8142 (t0) REVERT: C 155 MET cc_start: 0.6900 (tpp) cc_final: 0.6565 (tpp) REVERT: C 199 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6558 (m) REVERT: C 226 LEU cc_start: 0.6949 (mt) cc_final: 0.6664 (mt) REVERT: C 244 LEU cc_start: 0.7298 (mp) cc_final: 0.6593 (tp) REVERT: D 249 LYS cc_start: 0.5701 (tppt) cc_final: 0.4948 (tppt) REVERT: D 334 ARG cc_start: 0.8518 (ptt-90) cc_final: 0.8131 (ptt-90) REVERT: D 565 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7979 (mt-10) outliers start: 26 outliers final: 19 residues processed: 207 average time/residue: 0.6952 time to fit residues: 159.0842 Evaluate side-chains 203 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 565 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 52 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 181 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.197145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133499 restraints weight = 17473.265| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.93 r_work: 0.3273 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17360 Z= 0.105 Angle : 0.537 14.080 23532 Z= 0.274 Chirality : 0.039 0.174 2652 Planarity : 0.003 0.052 2948 Dihedral : 5.060 58.146 2316 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.30 % Allowed : 18.84 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.19), residues: 2076 helix: 0.37 (0.17), residues: 1160 sheet: 0.17 (0.36), residues: 208 loop : -2.21 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 540 TYR 0.010 0.001 TYR C 187 PHE 0.032 0.001 PHE C 150 TRP 0.028 0.001 TRP C 574 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00215 (17348) covalent geometry : angle 0.53445 (23508) SS BOND : bond 0.00325 ( 12) SS BOND : angle 1.59806 ( 24) hydrogen bonds : bond 0.05479 ( 691) hydrogen bonds : angle 3.80972 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6829.12 seconds wall clock time: 116 minutes 38.15 seconds (6998.15 seconds total)