Starting phenix.real_space_refine on Sat Jan 18 09:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uux_42600/01_2025/8uux_42600.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uux_42600/01_2025/8uux_42600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uux_42600/01_2025/8uux_42600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uux_42600/01_2025/8uux_42600.map" model { file = "/net/cci-nas-00/data/ceres_data/8uux_42600/01_2025/8uux_42600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uux_42600/01_2025/8uux_42600.cif" } resolution = 2.74 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= 0.003 sd= 0.475 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 48 5.16 5 C 7588 2.51 5 N 1938 2.21 5 O 2507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12084 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3949 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "B" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3953 Classifications: {'peptide': 515} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3869 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 458} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Time building chain proxies: 10.35, per 1000 atoms: 0.86 Number of scatterers: 12084 At special positions: 0 Unit cell: (118.8, 116.6, 124.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 48 16.00 O 2507 8.00 N 1938 7.00 C 7588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 22 sheets defined 9.5% alpha, 32.1% 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 37 through 42 removed outlier: 3.528A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.114A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.747A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 54 through 58 removed outlier: 4.114A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.752A pdb=" N PHE B 144 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.563A pdb=" N TRP B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.572A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.808A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 137 through 142 removed outlier: 4.087A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.731A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.579A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.629A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83 removed outlier: 7.176A pdb=" N ILE A 78 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 185 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A 80 " --> pdb=" O CYS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'A' and resid 447 through 451 removed outlier: 4.795A pdb=" N GLU A 447 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 447 through 451 removed outlier: 4.795A pdb=" N GLU A 447 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 485 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A 479 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG A 476 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL A 517 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG A 478 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE A 515 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 296 removed outlier: 4.384A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 379 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR A 354 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A 332 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY A 400 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN A 334 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 398 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU A 336 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 394 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLN A 340 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 392 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU A 342 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ARG A 390 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 69 removed outlier: 12.741A pdb=" N GLN B 61 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N SER B 207 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY B 65 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.781A pdb=" N CYS B 183 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 81 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 181 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.166A pdb=" N TYR B 99 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 218 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY B 101 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.559A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.559A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 497 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 485 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 479 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 487 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 268 through 269 removed outlier: 4.496A pdb=" N ARG B 268 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 289 through 298 removed outlier: 4.486A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 332 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 400 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN B 334 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 398 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 336 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 394 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 340 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 392 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU B 342 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ARG B 390 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 389 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.643A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.578A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AC1, first strand: chain 'C' and resid 448 through 451 Processing sheet with id=AC2, first strand: chain 'C' and resid 268 through 269 removed outlier: 4.545A pdb=" N ARG C 268 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 298 removed outlier: 6.785A pdb=" N PHE C 375 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE C 358 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 337 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 332 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY C 400 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN C 334 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 398 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU C 336 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 394 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN C 340 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG C 392 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 427 through 429 removed outlier: 5.139A pdb=" N SER C 500 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU C 488 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 485 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN C 479 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 487 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS C 489 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA C 472 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TRP C 520 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 828 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: 3.86 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3835 1.34 - 1.46: 2450 1.46 - 1.58: 5740 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12097 Sorted by residual: bond pdb=" CG GLN B 19 " pdb=" CD GLN B 19 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CB GLN B 19 " pdb=" CG GLN B 19 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CA VAL C 216 " pdb=" C VAL C 216 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.27e-02 6.20e+03 9.45e-01 bond pdb=" CA ASP B 20 " pdb=" C ASP B 20 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.80e-02 3.09e+03 9.35e-01 bond pdb=" N PRO B 31 " pdb=" CA PRO B 31 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.05e-01 ... (remaining 12092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16156 1.74 - 3.49: 383 3.49 - 5.23: 37 5.23 - 6.98: 6 6.98 - 8.72: 6 Bond angle restraints: 16588 Sorted by residual: angle pdb=" C GLN C 469 " pdb=" N SER C 470 " pdb=" CA SER C 470 " ideal model delta sigma weight residual 121.90 115.31 6.59 1.26e+00 6.30e-01 2.74e+01 angle pdb=" C GLN B 469 " pdb=" N SER B 470 " pdb=" CA SER B 470 " ideal model delta sigma weight residual 121.90 115.65 6.25 1.26e+00 6.30e-01 2.46e+01 angle pdb=" C LEU A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C PHE A 461 " pdb=" N ALA A 462 " pdb=" CA ALA A 462 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N GLY B 195 " pdb=" CA GLY B 195 " pdb=" C GLY B 195 " ideal model delta sigma weight residual 113.18 121.90 -8.72 2.37e+00 1.78e-01 1.35e+01 ... (remaining 16583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6363 17.64 - 35.28: 623 35.28 - 52.93: 131 52.93 - 70.57: 41 70.57 - 88.21: 15 Dihedral angle restraints: 7173 sinusoidal: 2753 harmonic: 4420 Sorted by residual: dihedral pdb=" CA THR C 363 " pdb=" C THR C 363 " pdb=" N ASN C 364 " pdb=" CA ASN C 364 " ideal model delta harmonic sigma weight residual 180.00 146.48 33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 147.37 32.63 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA ALA C 365 " pdb=" C ALA C 365 " pdb=" N ASP C 366 " pdb=" CA ASP C 366 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1119 0.031 - 0.063: 477 0.063 - 0.094: 151 0.094 - 0.125: 130 0.125 - 0.157: 11 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA ASP B 196 " pdb=" N ASP B 196 " pdb=" C ASP B 196 " pdb=" CB ASP B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA VAL C 414 " pdb=" N VAL C 414 " pdb=" C VAL C 414 " pdb=" CB VAL C 414 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA GLN A 28 " pdb=" N GLN A 28 " pdb=" C GLN A 28 " pdb=" CB GLN A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1885 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 128 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 129 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 219 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.49e+00 pdb=" N PRO C 220 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 193 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 194 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.027 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 344 2.69 - 3.24: 10251 3.24 - 3.79: 17529 3.79 - 4.35: 25488 4.35 - 4.90: 41767 Nonbonded interactions: 95379 Sorted by model distance: nonbonded pdb=" OG1 THR A 434 " pdb=" O HOH A 701 " model vdw 2.133 3.040 nonbonded pdb=" OE1 GLN A 312 " pdb=" O HOH A 702 " model vdw 2.196 3.040 nonbonded pdb=" O HOH A 709 " pdb=" O HOH A 799 " model vdw 2.212 3.040 nonbonded pdb=" O HOH A 703 " pdb=" O HOH A 709 " model vdw 2.214 3.040 nonbonded pdb=" O PRO A 248 " pdb=" O HOH A 701 " model vdw 2.224 3.040 ... (remaining 95374 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 531 or resid 601)) selection = (chain 'B' and (resid 29 through 531 or resid 601)) selection = chain 'C' } 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: 7.620 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.050 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.002 0.032 12097 Z= 0.160 Angle : 0.629 8.723 16588 Z= 0.342 Chirality : 0.045 0.157 1888 Planarity : 0.006 0.068 2172 Dihedral : 15.620 88.210 4339 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 0.95 % Allowed : 14.42 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.63 (0.19), residues: 1526 helix: -1.31 (0.57), residues: 56 sheet: -0.11 (0.25), residues: 396 loop : -1.55 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS B 170 PHE 0.014 0.001 PHE C 80 TYR 0.011 0.001 TYR B 227 ARG 0.002 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 488 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 197 GLU cc_start: 0.6759 (pm20) cc_final: 0.6334 (pp20) REVERT: C 176 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7409 (mt-10) REVERT: C 507 LEU cc_start: 0.8222 (tp) cc_final: 0.7974 (tp) outliers start: 12 outliers final: 10 residues processed: 165 average time/residue: 1.4200 time to fit residues: 252.8738 Evaluate side-chains 154 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 175 GLN B 402 GLN C 270 HIS C 340 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.170398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.148260 restraints weight = 11295.255| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 0.79 r_work: 0.3266 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work: 0.3102 rms_B_bonded: 2.75 restraints_weight: 0.1250 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12097 Z= 0.283 Angle : 0.725 11.283 16588 Z= 0.376 Chirality : 0.049 0.175 1888 Planarity : 0.007 0.069 2172 Dihedral : 6.351 57.197 1666 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 3.47 % Allowed : 13.00 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.53 (0.20), residues: 1526 helix: -1.08 (0.59), residues: 51 sheet: -0.10 (0.25), residues: 405 loop : -1.47 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 520 HIS 0.005 0.001 HIS B 170 PHE 0.028 0.002 PHE C 199 TYR 0.020 0.002 TYR B 227 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.396 Fit side-chains REVERT: A 100 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8636 (m) REVERT: A 148 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8647 (ttp) REVERT: A 488 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 19 GLN cc_start: 0.5899 (OUTLIER) cc_final: 0.5230 (mm110) REVERT: B 21 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7997 (pp) REVERT: B 197 GLU cc_start: 0.6734 (pm20) cc_final: 0.6335 (pp20) REVERT: C 155 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: C 176 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7714 (mt-10) REVERT: C 407 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: C 447 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 469 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7369 (mp10) outliers start: 44 outliers final: 19 residues processed: 180 average time/residue: 1.4623 time to fit residues: 283.3205 Evaluate side-chains 174 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN B 175 GLN B 261 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.169962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147553 restraints weight = 11455.833| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 0.82 r_work: 0.3251 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.3105 rms_B_bonded: 2.82 restraints_weight: 0.1250 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12097 Z= 0.297 Angle : 0.741 12.763 16588 Z= 0.383 Chirality : 0.050 0.176 1888 Planarity : 0.007 0.070 2172 Dihedral : 6.391 55.273 1662 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 4.33 % Allowed : 13.55 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.50 (0.20), residues: 1526 helix: -1.08 (0.62), residues: 51 sheet: -0.02 (0.25), residues: 405 loop : -1.48 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.005 0.001 HIS B 170 PHE 0.027 0.002 PHE C 199 TYR 0.021 0.002 TYR B 227 ARG 0.003 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 1.306 Fit side-chains REVERT: A 100 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8622 (m) REVERT: A 148 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8647 (ttp) REVERT: A 340 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 488 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 19 GLN cc_start: 0.5773 (OUTLIER) cc_final: 0.5128 (mm110) REVERT: B 21 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8112 (pp) REVERT: B 197 GLU cc_start: 0.6632 (pm20) cc_final: 0.6175 (pp20) REVERT: B 514 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 155 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: C 176 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7892 (mt-10) REVERT: C 407 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: C 447 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: C 469 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7429 (mp10) outliers start: 55 outliers final: 27 residues processed: 186 average time/residue: 1.4097 time to fit residues: 282.2383 Evaluate side-chains 183 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 64 optimal weight: 0.0070 chunk 52 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 402 GLN B 175 GLN B 261 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.171541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149448 restraints weight = 11381.086| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.79 r_work: 0.3269 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.3125 rms_B_bonded: 2.69 restraints_weight: 0.1250 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12097 Z= 0.214 Angle : 0.664 9.675 16588 Z= 0.344 Chirality : 0.047 0.162 1888 Planarity : 0.006 0.067 2172 Dihedral : 6.139 53.007 1662 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 3.31 % Allowed : 14.81 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.34 (0.20), residues: 1526 helix: -0.83 (0.65), residues: 51 sheet: 0.08 (0.25), residues: 415 loop : -1.38 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.004 0.001 HIS B 170 PHE 0.020 0.002 PHE C 199 TYR 0.018 0.001 TYR B 227 ARG 0.002 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.211 Fit side-chains REVERT: A 100 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8644 (m) REVERT: A 148 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8683 (ttp) REVERT: A 340 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 356 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: B 21 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7995 (pp) REVERT: B 197 GLU cc_start: 0.6556 (pm20) cc_final: 0.6131 (pp20) REVERT: B 514 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 155 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 176 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7973 (mt-10) REVERT: C 407 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 447 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: C 469 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7367 (mp10) outliers start: 42 outliers final: 23 residues processed: 179 average time/residue: 1.3955 time to fit residues: 270.4261 Evaluate side-chains 180 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 0.0270 chunk 121 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 3.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 402 GLN B 261 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.171009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.148391 restraints weight = 11344.572| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.80 r_work: 0.3239 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work: 0.3088 rms_B_bonded: 2.76 restraints_weight: 0.1250 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12097 Z= 0.252 Angle : 0.698 11.271 16588 Z= 0.359 Chirality : 0.048 0.168 1888 Planarity : 0.007 0.067 2172 Dihedral : 6.218 52.296 1662 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 4.18 % Allowed : 14.50 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.37 (0.20), residues: 1526 helix: -0.84 (0.66), residues: 51 sheet: 0.04 (0.25), residues: 408 loop : -1.38 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.004 0.001 HIS B 170 PHE 0.024 0.002 PHE C 199 TYR 0.019 0.002 TYR B 227 ARG 0.003 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.372 Fit side-chains REVERT: A 100 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8615 (m) REVERT: A 148 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8673 (ttp) REVERT: A 356 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: B 19 GLN cc_start: 0.5615 (OUTLIER) cc_final: 0.5014 (mm110) REVERT: B 21 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8016 (pp) REVERT: B 197 GLU cc_start: 0.6591 (pm20) cc_final: 0.6168 (pp20) REVERT: B 514 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 155 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 176 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7975 (mt-10) REVERT: C 407 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: C 447 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: C 469 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7447 (mp10) outliers start: 53 outliers final: 32 residues processed: 185 average time/residue: 1.4179 time to fit residues: 283.1817 Evaluate side-chains 188 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 30.0000 chunk 29 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 402 GLN B 175 GLN B 261 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.170194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.147024 restraints weight = 11541.079| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.84 r_work: 0.3228 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work: 0.3072 rms_B_bonded: 2.92 restraints_weight: 0.1250 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12097 Z= 0.298 Angle : 0.739 13.099 16588 Z= 0.380 Chirality : 0.050 0.179 1888 Planarity : 0.007 0.070 2172 Dihedral : 6.366 50.905 1662 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 4.10 % Allowed : 14.74 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.40 (0.20), residues: 1526 helix: -0.97 (0.65), residues: 51 sheet: 0.06 (0.25), residues: 408 loop : -1.42 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 520 HIS 0.005 0.001 HIS B 170 PHE 0.028 0.002 PHE C 199 TYR 0.021 0.002 TYR B 227 ARG 0.003 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 1.346 Fit side-chains REVERT: A 100 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8620 (m) REVERT: A 148 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8671 (ttp) REVERT: A 356 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: B 19 GLN cc_start: 0.5767 (OUTLIER) cc_final: 0.5148 (mm110) REVERT: B 21 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8058 (pp) REVERT: B 197 GLU cc_start: 0.6667 (pm20) cc_final: 0.6232 (pp20) REVERT: B 514 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8475 (mp) REVERT: C 155 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: C 176 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 396 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.7078 (ttm-80) REVERT: C 407 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: C 447 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: C 469 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7557 (mp10) outliers start: 52 outliers final: 31 residues processed: 186 average time/residue: 1.3882 time to fit residues: 278.7069 Evaluate side-chains 187 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 402 GLN A 479 ASN B 175 GLN B 261 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.170842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.147696 restraints weight = 11480.652| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 0.84 r_work: 0.3190 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work: 0.2834 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12097 Z= 0.259 Angle : 0.702 11.182 16588 Z= 0.362 Chirality : 0.048 0.172 1888 Planarity : 0.007 0.069 2172 Dihedral : 6.290 49.487 1662 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 4.10 % Allowed : 15.05 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.33 (0.20), residues: 1526 helix: -0.92 (0.65), residues: 51 sheet: 0.07 (0.24), residues: 430 loop : -1.37 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.005 0.001 HIS B 170 PHE 0.023 0.002 PHE C 199 TYR 0.019 0.002 TYR B 227 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.344 Fit side-chains REVERT: A 100 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8634 (m) REVERT: A 115 ASN cc_start: 0.7926 (m-40) cc_final: 0.7703 (m110) REVERT: A 148 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8739 (ttp) REVERT: A 356 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: B 19 GLN cc_start: 0.5680 (OUTLIER) cc_final: 0.5109 (mm110) REVERT: B 21 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8029 (pp) REVERT: B 197 GLU cc_start: 0.6725 (pm20) cc_final: 0.6244 (pp20) REVERT: B 514 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 155 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: C 176 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 396 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7183 (ttm-80) REVERT: C 407 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: C 447 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: C 469 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7706 (mp10) outliers start: 52 outliers final: 35 residues processed: 180 average time/residue: 1.4678 time to fit residues: 284.6726 Evaluate side-chains 192 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 0.0030 chunk 118 optimal weight: 0.0870 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN B 175 GLN B 261 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.175209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.153267 restraints weight = 11615.306| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 0.88 r_work: 0.3290 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.3138 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12097 Z= 0.134 Angle : 0.569 8.886 16588 Z= 0.294 Chirality : 0.044 0.146 1888 Planarity : 0.006 0.066 2172 Dihedral : 5.658 47.315 1662 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.36 % Rotamer: Outliers : 3.07 % Allowed : 16.23 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.14 (0.20), residues: 1526 helix: -1.03 (0.61), residues: 63 sheet: 0.11 (0.24), residues: 430 loop : -1.17 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS B 170 PHE 0.013 0.001 PHE C 80 TYR 0.011 0.001 TYR A 217 ARG 0.002 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.408 Fit side-chains REVERT: B 21 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7758 (pp) REVERT: B 514 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 155 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: C 176 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 340 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: C 396 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7056 (ttm-80) REVERT: C 407 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7957 (tm-30) outliers start: 39 outliers final: 19 residues processed: 179 average time/residue: 1.4277 time to fit residues: 277.1484 Evaluate side-chains 171 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 114 optimal weight: 0.0000 chunk 26 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 402 GLN B 340 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.173326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151359 restraints weight = 11480.506| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.85 r_work: 0.3292 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.3129 rms_B_bonded: 3.19 restraints_weight: 0.1250 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12097 Z= 0.188 Angle : 0.623 9.276 16588 Z= 0.320 Chirality : 0.046 0.170 1888 Planarity : 0.006 0.065 2172 Dihedral : 5.774 47.384 1662 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 2.21 % Allowed : 16.78 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.10 (0.20), residues: 1526 helix: -0.66 (0.64), residues: 57 sheet: 0.14 (0.24), residues: 419 loop : -1.16 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 520 HIS 0.004 0.001 HIS B 170 PHE 0.018 0.002 PHE C 199 TYR 0.017 0.001 TYR A 217 ARG 0.002 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.332 Fit side-chains REVERT: B 21 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7869 (pp) REVERT: C 155 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: C 176 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 396 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.7030 (ttm-80) REVERT: C 407 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8002 (tm-30) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 1.4273 time to fit residues: 261.8731 Evaluate side-chains 173 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 38 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 0.0270 overall best weight: 1.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 402 GLN B 340 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.174824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.151502 restraints weight = 11469.680| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 0.91 r_work: 0.3313 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3187 rms_B_bonded: 2.81 restraints_weight: 0.1250 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12097 Z= 0.148 Angle : 0.580 8.743 16588 Z= 0.298 Chirality : 0.045 0.144 1888 Planarity : 0.006 0.064 2172 Dihedral : 5.583 48.859 1661 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 2.21 % Allowed : 17.02 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1526 helix: -0.46 (0.65), residues: 57 sheet: 0.19 (0.24), residues: 423 loop : -1.09 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 170 PHE 0.013 0.001 PHE C 80 TYR 0.013 0.001 TYR A 217 ARG 0.002 0.000 ARG C 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.442 Fit side-chains REVERT: B 21 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7818 (pp) REVERT: B 514 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 155 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: C 176 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 407 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (tm-30) outliers start: 28 outliers final: 18 residues processed: 176 average time/residue: 1.3768 time to fit residues: 261.7782 Evaluate side-chains 172 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 402 GLN B 261 ASN B 340 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.173419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.151042 restraints weight = 11483.181| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 0.90 r_work: 0.3292 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work: 0.3155 rms_B_bonded: 2.98 restraints_weight: 0.1250 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12097 Z= 0.179 Angle : 0.616 9.050 16588 Z= 0.316 Chirality : 0.046 0.157 1888 Planarity : 0.006 0.064 2172 Dihedral : 5.702 49.066 1661 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 2.05 % Allowed : 17.26 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1526 helix: -0.62 (0.64), residues: 57 sheet: 0.21 (0.24), residues: 422 loop : -1.10 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.004 0.001 HIS B 170 PHE 0.016 0.002 PHE C 199 TYR 0.016 0.001 TYR A 217 ARG 0.002 0.000 ARG C 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10138.93 seconds wall clock time: 178 minutes 59.26 seconds (10739.26 seconds total)