Starting phenix.real_space_refine on Sun May 18 11:41:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j35_61106/05_2025/9j35_61106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j35_61106/05_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_61106/05_2025/9j35_61106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j35_61106/05_2025/9j35_61106.map" model { file = "/net/cci-nas-00/data/ceres_data/9j35_61106/05_2025/9j35_61106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j35_61106/05_2025/9j35_61106.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.45, per 1000 atoms: 0.56 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: 3.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.67 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: 4.40 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 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: 0.04 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: 2.120 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.200 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- 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 : 4.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.004 TRP C 373 HIS 0.012 0.003 HIS D 275 PHE 0.023 0.003 PHE B 171 TYR 0.033 0.004 TYR D 234 ARG 0.008 0.001 ARG D 169 Details of bonding type rmsd hydrogen bonds : bond 0.28151 ( 691) hydrogen bonds : angle 7.90873 ( 1944) SS BOND : bond 0.32529 ( 12) SS BOND : angle 14.00219 ( 24) covalent geometry : bond 0.01163 (17348) covalent geometry : angle 1.37119 (23508) *********************** 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 : 1.951 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: 1.4975 time to fit residues: 393.5833 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 : 1.745 ------------------------------------------------------------------------------- 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 175 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.194536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130625 restraints weight = 17580.482| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.93 r_work: 0.3258 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1510 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= 0.132 Angle : 0.629 8.152 23532 Z= 0.333 Chirality : 0.040 0.140 2652 Planarity : 0.005 0.066 2948 Dihedral : 6.040 55.630 2316 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.35 % Allowed : 11.50 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.16), residues: 2076 helix: -1.85 (0.14), residues: 1232 sheet: -2.04 (0.31), residues: 180 loop : -2.70 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 281 HIS 0.005 0.001 HIS C 275 PHE 0.014 0.001 PHE B 171 TYR 0.018 0.001 TYR C 187 ARG 0.005 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.07238 ( 691) hydrogen bonds : angle 4.61742 ( 1944) SS BOND : bond 0.00320 ( 12) SS BOND : angle 1.64402 ( 24) covalent geometry : bond 0.00266 (17348) covalent geometry : angle 0.62747 (23508) *********************** 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 239 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7832 (m-80) cc_final: 0.6928 (t80) REVERT: A 287 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: A 427 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8942 (mm-30) REVERT: A 486 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7106 (mtm-85) REVERT: B 112 PHE cc_start: 0.7845 (m-80) cc_final: 0.6981 (t80) REVERT: B 155 MET cc_start: 0.6281 (tmm) cc_final: 0.5426 (tmm) REVERT: B 287 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: B 415 MET cc_start: 0.8860 (tpp) cc_final: 0.8567 (tpp) REVERT: C 155 MET cc_start: 0.6622 (tpp) cc_final: 0.6316 (tpp) REVERT: C 287 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7958 (tp30) REVERT: D 108 ILE cc_start: 0.8555 (mt) cc_final: 0.8344 (mm) REVERT: D 235 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7486 (mp) REVERT: D 249 LYS cc_start: 0.6113 (tppt) cc_final: 0.5430 (tppt) REVERT: D 287 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: D 334 ARG cc_start: 0.8511 (ptt-90) cc_final: 0.8215 (ptt-90) REVERT: D 381 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8407 (mp) REVERT: D 415 MET cc_start: 0.8774 (tpp) cc_final: 0.8501 (tpp) outliers start: 25 outliers final: 8 residues processed: 229 average time/residue: 1.4337 time to fit residues: 362.3044 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 : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 486 ARG 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 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 103 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 114 optimal weight: 0.0070 chunk 154 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.194834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130707 restraints weight = 17444.877| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.93 r_work: 0.3244 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17360 Z= 0.124 Angle : 0.585 9.036 23532 Z= 0.307 Chirality : 0.040 0.138 2652 Planarity : 0.004 0.054 2948 Dihedral : 5.661 57.664 2316 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.16 % Allowed : 13.50 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.18), residues: 2076 helix: -0.96 (0.16), residues: 1180 sheet: -1.07 (0.32), residues: 220 loop : -2.44 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.006 0.001 HIS A 275 PHE 0.025 0.001 PHE A 150 TYR 0.015 0.001 TYR C 187 ARG 0.007 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.06659 ( 691) hydrogen bonds : angle 4.21894 ( 1944) SS BOND : bond 0.00468 ( 12) SS BOND : angle 2.07063 ( 24) covalent geometry : bond 0.00260 (17348) covalent geometry : angle 0.58147 (23508) *********************** 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 228 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7846 (m-80) cc_final: 0.6929 (t80) REVERT: A 415 MET cc_start: 0.8837 (tpp) cc_final: 0.8476 (tpp) REVERT: A 428 GLU cc_start: 0.8982 (tt0) cc_final: 0.8753 (mt-10) REVERT: A 533 ASP cc_start: 0.8586 (t0) cc_final: 0.8097 (t0) REVERT: B 112 PHE cc_start: 0.7851 (m-80) cc_final: 0.6996 (t80) REVERT: B 155 MET cc_start: 0.6146 (tmm) cc_final: 0.5251 (mtm) REVERT: B 428 GLU cc_start: 0.8944 (tt0) cc_final: 0.8527 (mt-10) REVERT: B 533 ASP cc_start: 0.8591 (t0) cc_final: 0.8081 (t0) REVERT: B 572 LEU cc_start: 0.7490 (tp) cc_final: 0.7265 (tp) REVERT: C 108 ILE cc_start: 0.8544 (mp) cc_final: 0.8330 (mp) REVERT: C 155 MET cc_start: 0.6577 (tpp) cc_final: 0.6110 (tpp) REVERT: C 287 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: D 108 ILE cc_start: 0.8399 (mt) cc_final: 0.8174 (mm) REVERT: D 235 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7245 (mp) REVERT: D 249 LYS cc_start: 0.5923 (tppt) cc_final: 0.5166 (tppt) REVERT: D 334 ARG cc_start: 0.8503 (ptt-90) cc_final: 0.8159 (ptt-90) REVERT: D 381 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 533 ASP cc_start: 0.8611 (t0) cc_final: 0.8408 (t70) outliers start: 40 outliers final: 21 residues processed: 209 average time/residue: 1.4380 time to fit residues: 331.8125 Evaluate side-chains 205 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 546 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 546 VAL 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 287 GLU 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 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 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 73 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 275 HIS B 416 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.191195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126464 restraints weight = 17483.614| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.92 r_work: 0.3193 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17360 Z= 0.201 Angle : 0.677 9.840 23532 Z= 0.353 Chirality : 0.044 0.149 2652 Planarity : 0.004 0.055 2948 Dihedral : 5.874 58.229 2316 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.62 % Allowed : 13.17 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2076 helix: -1.07 (0.15), residues: 1228 sheet: -1.33 (0.32), residues: 180 loop : -2.51 (0.19), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 574 HIS 0.009 0.002 HIS A 275 PHE 0.018 0.002 PHE B 171 TYR 0.016 0.002 TYR B 151 ARG 0.006 0.001 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.08867 ( 691) hydrogen bonds : angle 4.33297 ( 1944) SS BOND : bond 0.00439 ( 12) SS BOND : angle 2.25096 ( 24) covalent geometry : bond 0.00474 (17348) covalent geometry : angle 0.67348 (23508) *********************** 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 262 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7870 (m-80) cc_final: 0.6974 (t80) REVERT: A 400 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8935 (mt) REVERT: A 415 MET cc_start: 0.8776 (tpp) cc_final: 0.8455 (tpp) REVERT: A 416 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (tp40) REVERT: A 428 GLU cc_start: 0.8962 (tt0) cc_final: 0.8759 (mt-10) REVERT: A 486 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7130 (mtm-85) REVERT: A 533 ASP cc_start: 0.8639 (t0) cc_final: 0.8140 (t0) REVERT: B 112 PHE cc_start: 0.7853 (m-80) cc_final: 0.6985 (t80) REVERT: B 155 MET cc_start: 0.6154 (tmm) cc_final: 0.5204 (mtm) REVERT: B 244 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6918 (tp) REVERT: B 400 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 415 MET cc_start: 0.8775 (tpp) cc_final: 0.8515 (tpp) REVERT: B 416 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8544 (tp40) REVERT: B 428 GLU cc_start: 0.8974 (tt0) cc_final: 0.8742 (mt-10) REVERT: B 533 ASP cc_start: 0.8642 (t0) cc_final: 0.8122 (t0) REVERT: C 155 MET cc_start: 0.6546 (tpp) cc_final: 0.6091 (tpp) REVERT: C 287 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: C 381 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8458 (mp) REVERT: C 400 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8914 (mt) REVERT: D 108 ILE cc_start: 0.8409 (mt) cc_final: 0.8189 (mm) REVERT: D 171 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.4285 (p90) REVERT: D 189 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: D 235 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7259 (mp) REVERT: D 249 LYS cc_start: 0.5933 (tppt) cc_final: 0.5131 (tppt) REVERT: D 330 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8109 (ttpp) REVERT: D 334 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.8149 (ptt-90) REVERT: D 381 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8554 (mp) REVERT: D 400 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8942 (mt) REVERT: D 415 MET cc_start: 0.8761 (tpp) cc_final: 0.8487 (tpp) REVERT: D 495 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.7221 (mmm160) REVERT: D 533 ASP cc_start: 0.8651 (t0) cc_final: 0.8419 (t70) outliers start: 67 outliers final: 32 residues processed: 245 average time/residue: 1.3257 time to fit residues: 360.7040 Evaluate side-chains 235 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 ARG 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 244 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 520 THR 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 206 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU 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 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 189 GLN 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 235 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 330 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 9 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 157 optimal weight: 0.2980 chunk 184 optimal weight: 0.9980 chunk 82 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 416 GLN ** 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 = 0.4134 r_free = 0.4134 target = 0.196014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132785 restraints weight = 17679.640| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.24 r_work: 0.3224 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2060 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= 0.108 Angle : 0.541 9.082 23532 Z= 0.285 Chirality : 0.039 0.135 2652 Planarity : 0.004 0.052 2948 Dihedral : 5.441 59.179 2316 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.65 % Allowed : 15.01 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.18), residues: 2076 helix: -0.36 (0.16), residues: 1160 sheet: -0.53 (0.33), residues: 220 loop : -2.33 (0.19), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.005 0.001 HIS A 275 PHE 0.028 0.001 PHE C 150 TYR 0.015 0.001 TYR C 187 ARG 0.005 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.05861 ( 691) hydrogen bonds : angle 4.00410 ( 1944) SS BOND : bond 0.00262 ( 12) SS BOND : angle 1.60882 ( 24) covalent geometry : bond 0.00213 (17348) covalent geometry : angle 0.53914 (23508) *********************** 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 245 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7861 (m-80) cc_final: 0.6894 (t80) REVERT: A 199 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6401 (m) REVERT: A 416 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: A 428 GLU cc_start: 0.8996 (tt0) cc_final: 0.8624 (mt-10) REVERT: A 429 MET cc_start: 0.9138 (tmm) cc_final: 0.8929 (ttp) REVERT: A 533 ASP cc_start: 0.8615 (t0) cc_final: 0.8129 (t0) REVERT: B 112 PHE cc_start: 0.7830 (m-80) cc_final: 0.6951 (t80) REVERT: B 155 MET cc_start: 0.6091 (tmm) cc_final: 0.5201 (mtm) REVERT: B 244 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6958 (tp) REVERT: B 416 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8551 (tp40) REVERT: B 428 GLU cc_start: 0.8900 (tt0) cc_final: 0.8574 (mt-10) REVERT: B 506 LEU cc_start: 0.7533 (tp) cc_final: 0.7251 (mt) REVERT: B 533 ASP cc_start: 0.8601 (t0) cc_final: 0.8117 (t0) REVERT: C 155 MET cc_start: 0.6807 (tpp) cc_final: 0.6267 (tpp) REVERT: C 199 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6547 (m) REVERT: C 614 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5909 (m-10) REVERT: D 108 ILE cc_start: 0.8339 (mt) cc_final: 0.8123 (mm) REVERT: D 171 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.4088 (p90) REVERT: D 189 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: D 249 LYS cc_start: 0.5782 (tppt) cc_final: 0.4978 (tppt) REVERT: D 334 ARG cc_start: 0.8488 (ptt-90) cc_final: 0.8101 (ptt-90) REVERT: D 533 ASP cc_start: 0.8643 (t0) cc_final: 0.8427 (t70) outliers start: 49 outliers final: 23 residues processed: 234 average time/residue: 1.3530 time to fit residues: 350.0169 Evaluate side-chains 221 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE 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 416 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 416 GLN 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 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 C residue 614 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 206 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 520 THR Chi-restraints excluded: chain D residue 546 VAL 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 122 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 105 optimal weight: 0.0370 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 416 GLN B 383 GLN B 416 GLN ** D 158 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 = 0.4110 r_free = 0.4110 target = 0.193488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133657 restraints weight = 17570.634| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.21 r_work: 0.3148 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17360 Z= 0.145 Angle : 0.597 10.720 23532 Z= 0.310 Chirality : 0.041 0.158 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.497 59.785 2316 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.75 % Allowed : 15.77 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 2076 helix: -0.44 (0.16), residues: 1192 sheet: -0.37 (0.33), residues: 220 loop : -2.42 (0.19), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 574 HIS 0.007 0.001 HIS D 275 PHE 0.012 0.001 PHE B 171 TYR 0.012 0.002 TYR C 187 ARG 0.005 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.07234 ( 691) hydrogen bonds : angle 4.05903 ( 1944) SS BOND : bond 0.00293 ( 12) SS BOND : angle 2.28357 ( 24) covalent geometry : bond 0.00327 (17348) covalent geometry : angle 0.59322 (23508) *********************** 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 240 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7806 (m-80) cc_final: 0.6924 (t80) REVERT: A 199 VAL cc_start: 0.6802 (OUTLIER) cc_final: 0.6380 (m) REVERT: A 416 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: A 428 GLU cc_start: 0.8885 (tt0) cc_final: 0.8509 (mt-10) REVERT: A 533 ASP cc_start: 0.8556 (t0) cc_final: 0.8057 (t0) REVERT: B 112 PHE cc_start: 0.7765 (m-80) cc_final: 0.6910 (t80) REVERT: B 155 MET cc_start: 0.5953 (tmm) cc_final: 0.5147 (mtm) REVERT: B 416 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8558 (tp40) REVERT: B 428 GLU cc_start: 0.8814 (tt0) cc_final: 0.8444 (mt-10) REVERT: B 504 ASP cc_start: 0.7193 (t0) cc_final: 0.6799 (t0) REVERT: B 506 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7123 (mp) REVERT: B 533 ASP cc_start: 0.8564 (t0) cc_final: 0.8065 (t0) REVERT: C 155 MET cc_start: 0.6718 (tpp) cc_final: 0.6298 (tpp) REVERT: D 108 ILE cc_start: 0.8301 (mt) cc_final: 0.8076 (mm) REVERT: D 171 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.4235 (p90) REVERT: D 189 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: D 235 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7264 (mp) REVERT: D 249 LYS cc_start: 0.5954 (tppt) cc_final: 0.5210 (tppt) REVERT: D 334 ARG cc_start: 0.8429 (ptt-90) cc_final: 0.8050 (ptt-90) REVERT: D 381 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8506 (mp) REVERT: D 533 ASP cc_start: 0.8602 (t0) cc_final: 0.8384 (t70) outliers start: 51 outliers final: 29 residues processed: 230 average time/residue: 1.3552 time to fit residues: 344.8371 Evaluate side-chains 224 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS 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 416 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 206 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 416 GLN Chi-restraints excluded: chain B residue 506 LEU 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 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 189 GLN 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 235 ILE 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 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 78 optimal weight: 1.9990 chunk 205 optimal weight: 0.0270 chunk 123 optimal weight: 4.9990 chunk 96 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 416 GLN ** 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 = 0.4143 r_free = 0.4143 target = 0.196897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133310 restraints weight = 17557.479| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.94 r_work: 0.3269 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17360 Z= 0.100 Angle : 0.529 11.411 23532 Z= 0.274 Chirality : 0.039 0.142 2652 Planarity : 0.003 0.051 2948 Dihedral : 5.216 59.723 2316 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.48 % Allowed : 16.31 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2076 helix: 0.05 (0.17), residues: 1160 sheet: -0.19 (0.33), residues: 220 loop : -2.30 (0.19), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.004 0.001 HIS D 275 PHE 0.029 0.001 PHE C 150 TYR 0.013 0.001 TYR C 187 ARG 0.004 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.05327 ( 691) hydrogen bonds : angle 3.85597 ( 1944) SS BOND : bond 0.00269 ( 12) SS BOND : angle 1.80264 ( 24) covalent geometry : bond 0.00199 (17348) covalent geometry : angle 0.52570 (23508) *********************** 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 241 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7826 (m-80) cc_final: 0.6903 (t80) REVERT: A 199 VAL cc_start: 0.6799 (OUTLIER) cc_final: 0.6374 (m) REVERT: A 416 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7867 (tp40) REVERT: A 429 MET cc_start: 0.9105 (tmm) cc_final: 0.8889 (ttp) REVERT: A 533 ASP cc_start: 0.8583 (t0) cc_final: 0.8110 (t0) REVERT: B 112 PHE cc_start: 0.7798 (m-80) cc_final: 0.6966 (t80) REVERT: B 155 MET cc_start: 0.5991 (tmm) cc_final: 0.5124 (mtm) REVERT: B 415 MET cc_start: 0.8732 (tpp) cc_final: 0.8459 (tpp) REVERT: B 416 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8553 (tp40) REVERT: B 428 GLU cc_start: 0.8849 (tt0) cc_final: 0.8576 (mt-10) REVERT: B 504 ASP cc_start: 0.7013 (t0) cc_final: 0.6649 (t0) REVERT: B 533 ASP cc_start: 0.8584 (t0) cc_final: 0.8118 (t0) REVERT: C 108 ILE cc_start: 0.8353 (mp) cc_final: 0.8029 (mp) REVERT: C 155 MET cc_start: 0.6873 (tpp) cc_final: 0.6440 (tpp) REVERT: C 199 VAL cc_start: 0.6968 (OUTLIER) cc_final: 0.6551 (m) REVERT: C 287 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: C 528 GLU cc_start: 0.7034 (tt0) cc_final: 0.6824 (mt-10) REVERT: D 108 ILE cc_start: 0.8322 (mt) cc_final: 0.8105 (mm) REVERT: D 171 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.4046 (p90) REVERT: D 189 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6202 (tm-30) REVERT: D 249 LYS cc_start: 0.5716 (tppt) cc_final: 0.4978 (tppt) REVERT: D 334 ARG cc_start: 0.8452 (ptt-90) cc_final: 0.8073 (ptt-90) REVERT: D 533 ASP cc_start: 0.8606 (t0) cc_final: 0.8392 (t70) outliers start: 46 outliers final: 30 residues processed: 231 average time/residue: 1.3597 time to fit residues: 348.2341 Evaluate side-chains 225 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 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 416 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 206 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 416 GLN 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 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 287 GLU 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 D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 189 GLN 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 546 VAL 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 193 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 162 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 204 optimal weight: 0.0470 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.196194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133539 restraints weight = 17494.342| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.23 r_work: 0.3231 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17360 Z= 0.112 Angle : 0.545 12.073 23532 Z= 0.281 Chirality : 0.039 0.151 2652 Planarity : 0.003 0.051 2948 Dihedral : 5.174 59.284 2316 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.59 % Allowed : 16.41 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2076 helix: 0.15 (0.17), residues: 1160 sheet: -0.09 (0.33), residues: 220 loop : -2.25 (0.19), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 574 HIS 0.005 0.001 HIS A 275 PHE 0.010 0.001 PHE C 103 TYR 0.011 0.001 TYR C 187 ARG 0.007 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.05820 ( 691) hydrogen bonds : angle 3.85523 ( 1944) SS BOND : bond 0.00275 ( 12) SS BOND : angle 1.74548 ( 24) covalent geometry : bond 0.00237 (17348) covalent geometry : angle 0.54233 (23508) *********************** 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 233 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7865 (m-80) cc_final: 0.6891 (t80) REVERT: A 199 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6362 (m) REVERT: A 287 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: A 416 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (tp-100) REVERT: A 428 GLU cc_start: 0.8947 (tt0) cc_final: 0.8652 (mt-10) REVERT: A 504 ASP cc_start: 0.7136 (t0) cc_final: 0.6824 (t0) REVERT: A 533 ASP cc_start: 0.8621 (t0) cc_final: 0.8135 (t0) REVERT: B 112 PHE cc_start: 0.7829 (m-80) cc_final: 0.6922 (t80) REVERT: B 155 MET cc_start: 0.5932 (tmm) cc_final: 0.5008 (mtm) REVERT: B 287 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 415 MET cc_start: 0.8746 (tpp) cc_final: 0.8478 (tpp) REVERT: B 428 GLU cc_start: 0.8937 (tt0) cc_final: 0.8631 (mt-10) REVERT: B 504 ASP cc_start: 0.6969 (t0) cc_final: 0.6614 (t0) REVERT: B 533 ASP cc_start: 0.8608 (t0) cc_final: 0.8139 (t0) REVERT: B 569 GLU cc_start: 0.8300 (pm20) cc_final: 0.8004 (pm20) REVERT: C 155 MET cc_start: 0.6901 (tpp) cc_final: 0.6468 (tpp) REVERT: C 204 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5624 (mp10) REVERT: C 528 GLU cc_start: 0.6986 (tt0) cc_final: 0.6779 (mt-10) REVERT: D 108 ILE cc_start: 0.8284 (mt) cc_final: 0.8068 (mm) REVERT: D 171 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.4059 (p90) REVERT: D 189 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: D 249 LYS cc_start: 0.5700 (tppt) cc_final: 0.4962 (tppt) REVERT: D 287 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: D 334 ARG cc_start: 0.8473 (ptt-90) cc_final: 0.8088 (ptt-90) REVERT: D 533 ASP cc_start: 0.8665 (t0) cc_final: 0.8445 (t70) outliers start: 48 outliers final: 29 residues processed: 224 average time/residue: 1.4007 time to fit residues: 346.7893 Evaluate side-chains 220 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 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 287 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 287 GLU 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 C residue 145 THR Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR 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 D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 189 GLN 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 287 GLU 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 546 VAL Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 202 optimal weight: 7.9990 chunk 11 optimal weight: 0.0060 chunk 20 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.194470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134190 restraints weight = 17589.628| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.21 r_work: 0.3187 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17360 Z= 0.136 Angle : 0.579 13.648 23532 Z= 0.299 Chirality : 0.041 0.166 2652 Planarity : 0.004 0.051 2948 Dihedral : 5.260 58.779 2316 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.38 % Allowed : 16.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2076 helix: 0.09 (0.17), residues: 1156 sheet: -0.26 (0.33), residues: 228 loop : -2.31 (0.19), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 574 HIS 0.007 0.001 HIS A 275 PHE 0.031 0.001 PHE C 150 TYR 0.010 0.001 TYR C 270 ARG 0.007 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.06847 ( 691) hydrogen bonds : angle 3.96512 ( 1944) SS BOND : bond 0.00273 ( 12) SS BOND : angle 1.83032 ( 24) covalent geometry : bond 0.00302 (17348) covalent geometry : angle 0.57675 (23508) *********************** 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 225 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7755 (m-80) cc_final: 0.6891 (t80) REVERT: A 199 VAL cc_start: 0.6745 (OUTLIER) cc_final: 0.6322 (m) REVERT: A 416 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7964 (tp40) REVERT: A 428 GLU cc_start: 0.8803 (tt0) cc_final: 0.8527 (mt-10) REVERT: A 504 ASP cc_start: 0.7091 (t0) cc_final: 0.6773 (t0) REVERT: A 533 ASP cc_start: 0.8581 (t0) cc_final: 0.8069 (t0) REVERT: B 112 PHE cc_start: 0.7738 (m-80) cc_final: 0.6886 (t80) REVERT: B 155 MET cc_start: 0.6007 (tmm) cc_final: 0.5016 (mtm) REVERT: B 287 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: B 504 ASP cc_start: 0.6954 (t0) cc_final: 0.6611 (t0) REVERT: B 533 ASP cc_start: 0.8562 (t0) cc_final: 0.8072 (t0) REVERT: B 569 GLU cc_start: 0.8246 (pm20) cc_final: 0.7962 (pm20) REVERT: C 108 ILE cc_start: 0.8344 (mp) cc_final: 0.8015 (mp) REVERT: C 155 MET cc_start: 0.6789 (tpp) cc_final: 0.6375 (tpp) REVERT: C 199 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6569 (m) REVERT: C 204 GLN cc_start: 0.5950 (OUTLIER) cc_final: 0.5643 (mp10) REVERT: D 108 ILE cc_start: 0.8261 (mt) cc_final: 0.8038 (mm) REVERT: D 171 PHE cc_start: 0.6337 (OUTLIER) cc_final: 0.4195 (p90) REVERT: D 189 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: D 249 LYS cc_start: 0.5945 (tppt) cc_final: 0.5199 (tppt) REVERT: D 334 ARG cc_start: 0.8370 (ptt-90) cc_final: 0.8004 (ptt-90) REVERT: D 533 ASP cc_start: 0.8560 (t0) cc_final: 0.8339 (t70) outliers start: 44 outliers final: 31 residues processed: 220 average time/residue: 1.3240 time to fit residues: 322.8570 Evaluate side-chains 218 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 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 416 GLN 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 206 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 287 GLU 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 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 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 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 189 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.195692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131770 restraints weight = 17606.206| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.93 r_work: 0.3260 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17360 Z= 0.114 Angle : 0.557 13.924 23532 Z= 0.285 Chirality : 0.040 0.169 2652 Planarity : 0.004 0.050 2948 Dihedral : 5.154 58.568 2316 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.11 % Allowed : 17.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2076 helix: 0.21 (0.17), residues: 1160 sheet: -0.18 (0.33), residues: 228 loop : -2.24 (0.19), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 574 HIS 0.006 0.001 HIS A 275 PHE 0.015 0.001 PHE C 566 TYR 0.010 0.001 TYR C 187 ARG 0.006 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.06024 ( 691) hydrogen bonds : angle 3.90153 ( 1944) SS BOND : bond 0.00268 ( 12) SS BOND : angle 1.74028 ( 24) covalent geometry : bond 0.00238 (17348) covalent geometry : angle 0.55410 (23508) ********************** 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 224 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7828 (m-80) cc_final: 0.6913 (t80) REVERT: A 199 VAL cc_start: 0.6720 (OUTLIER) cc_final: 0.6299 (m) REVERT: A 416 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8159 (tp40) REVERT: A 428 GLU cc_start: 0.8928 (tt0) cc_final: 0.8657 (mt-10) REVERT: A 504 ASP cc_start: 0.6990 (t0) cc_final: 0.6690 (t0) REVERT: A 533 ASP cc_start: 0.8625 (t0) cc_final: 0.8115 (t0) REVERT: B 112 PHE cc_start: 0.7832 (m-80) cc_final: 0.6966 (t80) REVERT: B 155 MET cc_start: 0.5938 (tmm) cc_final: 0.5049 (mtm) REVERT: B 287 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: B 428 GLU cc_start: 0.8902 (tt0) cc_final: 0.8636 (mt-10) REVERT: B 504 ASP cc_start: 0.6974 (t0) cc_final: 0.6632 (t0) REVERT: B 533 ASP cc_start: 0.8596 (t0) cc_final: 0.8124 (t0) REVERT: B 569 GLU cc_start: 0.8246 (pm20) cc_final: 0.7959 (pm20) REVERT: C 108 ILE cc_start: 0.8367 (mp) cc_final: 0.8035 (mp) REVERT: C 155 MET cc_start: 0.6867 (tpp) cc_final: 0.6425 (tpp) REVERT: C 199 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6581 (m) REVERT: C 226 LEU cc_start: 0.7038 (mt) cc_final: 0.6730 (mt) REVERT: C 244 LEU cc_start: 0.7347 (mp) cc_final: 0.6615 (tp) REVERT: D 108 ILE cc_start: 0.8318 (mt) cc_final: 0.8104 (mm) REVERT: D 171 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.4227 (p90) REVERT: D 189 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6367 (tm-30) REVERT: D 249 LYS cc_start: 0.5769 (tppt) cc_final: 0.5027 (tppt) REVERT: D 334 ARG cc_start: 0.8434 (ptt-90) cc_final: 0.8066 (ptt-90) REVERT: D 533 ASP cc_start: 0.8617 (t0) cc_final: 0.8399 (t70) outliers start: 39 outliers final: 31 residues processed: 217 average time/residue: 1.3516 time to fit residues: 324.8925 Evaluate side-chains 220 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 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 416 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 287 GLU 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 C residue 145 THR Chi-restraints excluded: chain C residue 199 VAL 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 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 189 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 22 optimal weight: 0.7980 chunk 202 optimal weight: 0.0370 chunk 30 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.197860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136845 restraints weight = 17568.136| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.16 r_work: 0.3275 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17360 Z= 0.098 Angle : 0.528 13.648 23532 Z= 0.269 Chirality : 0.039 0.166 2652 Planarity : 0.003 0.051 2948 Dihedral : 4.989 58.638 2316 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.78 % Allowed : 17.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 2076 helix: 0.40 (0.17), residues: 1164 sheet: 0.08 (0.36), residues: 208 loop : -2.13 (0.18), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 574 HIS 0.004 0.001 HIS A 275 PHE 0.031 0.001 PHE C 150 TYR 0.010 0.001 TYR B 282 ARG 0.006 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 691) hydrogen bonds : angle 3.79352 ( 1944) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.61942 ( 24) covalent geometry : bond 0.00196 (17348) covalent geometry : angle 0.52551 (23508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13391.51 seconds wall clock time: 230 minutes 30.49 seconds (13830.49 seconds total)