Starting phenix.real_space_refine on Tue Aug 26 00:44:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghd_40041/08_2025/8ghd_40041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghd_40041/08_2025/8ghd_40041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ghd_40041/08_2025/8ghd_40041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghd_40041/08_2025/8ghd_40041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghd_40041/08_2025/8ghd_40041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghd_40041/08_2025/8ghd_40041.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 2.275 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 Fe 6 7.16 5 S 216 5.16 5 C 20616 2.51 5 N 5580 2.21 5 O 5802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "B" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "C" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "D" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "E" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "F" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'ACD': 1, 'FE2': 1, 'ZR5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.43, per 1000 atoms: 0.26 Number of scatterers: 32220 At special positions: 0 Unit cell: (153.34, 149.24, 104.14, 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) Fe 6 26.01 S 216 16.00 O 5802 8.00 N 5580 7.00 C 20616 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: 2.70 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 30 sheets defined 51.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 167 through 192 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 224 through 235 removed outlier: 4.068A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 336 through 358 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.765A pdb=" N ARG A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 458 through 483 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 583 through 599 Processing helix chain 'A' and resid 617 through 643 removed outlier: 3.716A pdb=" N LYS A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 139 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 167 through 192 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 224 through 235 removed outlier: 4.064A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 336 through 358 Processing helix chain 'B' and resid 364 through 379 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 391 through 394 removed outlier: 3.765A pdb=" N ARG B 394 " --> pdb=" O PRO B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 442 through 450 Processing helix chain 'B' and resid 458 through 483 Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 492 through 504 Processing helix chain 'B' and resid 521 through 537 Processing helix chain 'B' and resid 537 through 545 Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 583 through 599 Processing helix chain 'B' and resid 617 through 643 removed outlier: 3.722A pdb=" N LYS B 621 " --> pdb=" O GLY B 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 139 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 167 through 192 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 212 through 222 Processing helix chain 'C' and resid 224 through 235 removed outlier: 4.070A pdb=" N PHE C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 279 through 282 Processing helix chain 'C' and resid 336 through 358 Processing helix chain 'C' and resid 364 through 379 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 391 through 394 removed outlier: 3.764A pdb=" N ARG C 394 " --> pdb=" O PRO C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 395 through 407 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 438 through 441 Processing helix chain 'C' and resid 442 through 450 Processing helix chain 'C' and resid 458 through 483 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 492 through 504 Processing helix chain 'C' and resid 521 through 537 Processing helix chain 'C' and resid 537 through 545 Processing helix chain 'C' and resid 546 through 552 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 573 through 581 Processing helix chain 'C' and resid 583 through 599 Processing helix chain 'C' and resid 617 through 643 removed outlier: 3.723A pdb=" N LYS C 621 " --> pdb=" O GLY C 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 139 Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 167 through 192 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 224 through 235 removed outlier: 4.066A pdb=" N PHE D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 279 through 282 Processing helix chain 'D' and resid 336 through 358 Processing helix chain 'D' and resid 364 through 379 Processing helix chain 'D' and resid 383 through 390 Processing helix chain 'D' and resid 391 through 394 removed outlier: 3.767A pdb=" N ARG D 394 " --> pdb=" O PRO D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 423 through 435 Processing helix chain 'D' and resid 438 through 441 Processing helix chain 'D' and resid 442 through 450 Processing helix chain 'D' and resid 458 through 483 Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 492 through 504 Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 537 through 545 Processing helix chain 'D' and resid 546 through 552 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 573 through 581 Processing helix chain 'D' and resid 583 through 599 Processing helix chain 'D' and resid 617 through 643 removed outlier: 3.714A pdb=" N LYS D 621 " --> pdb=" O GLY D 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 139 Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 167 through 192 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 199 through 206 Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 224 through 235 removed outlier: 4.073A pdb=" N PHE E 232 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 270 Processing helix chain 'E' and resid 279 through 282 Processing helix chain 'E' and resid 336 through 358 Processing helix chain 'E' and resid 364 through 379 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 391 through 394 removed outlier: 3.761A pdb=" N ARG E 394 " --> pdb=" O PRO E 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 391 through 394' Processing helix chain 'E' and resid 395 through 407 Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 423 through 435 Processing helix chain 'E' and resid 438 through 441 Processing helix chain 'E' and resid 442 through 450 Processing helix chain 'E' and resid 458 through 483 Processing helix chain 'E' and resid 485 through 491 Processing helix chain 'E' and resid 492 through 504 Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 537 through 545 Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 553 through 557 Processing helix chain 'E' and resid 573 through 581 Processing helix chain 'E' and resid 583 through 599 Processing helix chain 'E' and resid 617 through 643 removed outlier: 3.715A pdb=" N LYS E 621 " --> pdb=" O GLY E 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 167 through 192 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 199 through 206 Processing helix chain 'F' and resid 212 through 222 Processing helix chain 'F' and resid 224 through 235 removed outlier: 4.076A pdb=" N PHE F 232 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 233 " --> pdb=" O SER F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 270 Processing helix chain 'F' and resid 279 through 282 Processing helix chain 'F' and resid 336 through 358 Processing helix chain 'F' and resid 364 through 379 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 391 through 394 removed outlier: 3.761A pdb=" N ARG F 394 " --> pdb=" O PRO F 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 391 through 394' Processing helix chain 'F' and resid 395 through 407 Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'F' and resid 423 through 435 Processing helix chain 'F' and resid 438 through 441 Processing helix chain 'F' and resid 442 through 450 Processing helix chain 'F' and resid 458 through 483 Processing helix chain 'F' and resid 485 through 491 Processing helix chain 'F' and resid 492 through 504 Processing helix chain 'F' and resid 521 through 537 Processing helix chain 'F' and resid 537 through 545 Processing helix chain 'F' and resid 546 through 552 Processing helix chain 'F' and resid 553 through 557 Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'F' and resid 583 through 599 Processing helix chain 'F' and resid 617 through 643 removed outlier: 3.722A pdb=" N LYS F 621 " --> pdb=" O GLY F 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 52 removed outlier: 5.104A pdb=" N GLY A 11 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS A 78 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP A 13 " --> pdb=" O TRP A 76 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP A 76 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 77 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 98 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 79 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 7.242A pdb=" N ARG A 21 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS A 67 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN A 23 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 65 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP A 25 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 63 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 removed outlier: 6.634A pdb=" N LEU A 300 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET A 302 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 5.105A pdb=" N GLY B 11 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS B 78 " --> pdb=" O GLY B 11 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 13 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP B 76 " --> pdb=" O TRP B 13 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 77 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG B 98 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 79 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 38 removed outlier: 7.250A pdb=" N ARG B 21 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS B 67 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN B 23 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 65 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP B 25 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 63 " --> pdb=" O TRP B 25 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 27 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.633A pdb=" N LEU B 300 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET B 302 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AB2, first strand: chain 'C' and resid 47 through 52 removed outlier: 5.108A pdb=" N GLY C 11 " --> pdb=" O CYS C 78 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS C 78 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 13 " --> pdb=" O TRP C 76 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP C 76 " --> pdb=" O TRP C 13 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE C 77 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG C 98 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP C 79 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 38 removed outlier: 7.246A pdb=" N ARG C 21 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS C 67 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN C 23 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU C 65 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP C 25 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL C 63 " --> pdb=" O TRP C 25 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 removed outlier: 6.633A pdb=" N LEU C 300 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 316 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET C 302 " --> pdb=" O MET C 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 288 through 289 Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.108A pdb=" N GLY D 11 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS D 78 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP D 13 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP D 76 " --> pdb=" O TRP D 13 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE D 77 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG D 98 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP D 79 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 32 through 38 removed outlier: 7.243A pdb=" N ARG D 21 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS D 67 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN D 23 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU D 65 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP D 25 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 63 " --> pdb=" O TRP D 25 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL D 27 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AC1, first strand: chain 'D' and resid 242 through 243 removed outlier: 6.633A pdb=" N LEU D 300 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE D 316 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET D 302 " --> pdb=" O MET D 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 288 through 289 Processing sheet with id=AC3, first strand: chain 'E' and resid 47 through 52 removed outlier: 5.104A pdb=" N GLY E 11 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS E 78 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP E 13 " --> pdb=" O TRP E 76 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP E 76 " --> pdb=" O TRP E 13 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE E 77 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG E 98 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP E 79 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 32 through 38 removed outlier: 7.232A pdb=" N ARG E 21 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS E 67 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN E 23 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU E 65 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP E 25 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 63 " --> pdb=" O TRP E 25 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL E 27 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AC6, first strand: chain 'E' and resid 242 through 243 removed outlier: 6.639A pdb=" N LEU E 300 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE E 316 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET E 302 " --> pdb=" O MET E 314 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 288 through 289 Processing sheet with id=AC8, first strand: chain 'F' and resid 47 through 52 removed outlier: 5.100A pdb=" N GLY F 11 " --> pdb=" O CYS F 78 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N CYS F 78 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP F 13 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP F 76 " --> pdb=" O TRP F 13 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE F 77 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG F 98 " --> pdb=" O PHE F 77 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP F 79 " --> pdb=" O CYS F 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 32 through 38 removed outlier: 7.240A pdb=" N ARG F 21 " --> pdb=" O LYS F 67 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS F 67 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN F 23 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU F 65 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TRP F 25 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL F 63 " --> pdb=" O TRP F 25 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 27 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AD2, first strand: chain 'F' and resid 242 through 243 removed outlier: 6.637A pdb=" N LEU F 300 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE F 316 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET F 302 " --> pdb=" O MET F 314 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 288 through 289 1620 hydrogen bonds defined for protein. 4533 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: 7.65 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10425 1.34 - 1.46: 5997 1.46 - 1.58: 16320 1.58 - 1.69: 6 1.69 - 1.81: 324 Bond restraints: 33072 Sorted by residual: bond pdb=" C PRO E 443 " pdb=" N PRO E 444 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.36e-02 5.41e+03 5.13e+00 bond pdb=" C PRO F 443 " pdb=" N PRO F 444 " ideal model delta sigma weight residual 1.335 1.366 -0.030 1.36e-02 5.41e+03 4.93e+00 bond pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.88e+00 bond pdb=" C PRO C 443 " pdb=" N PRO C 444 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.72e+00 bond pdb=" C PRO B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.36e-02 5.41e+03 4.70e+00 ... (remaining 33067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 43355 2.00 - 4.01: 1321 4.01 - 6.01: 186 6.01 - 8.02: 26 8.02 - 10.02: 34 Bond angle restraints: 44922 Sorted by residual: angle pdb=" N PRO E 443 " pdb=" CA PRO E 443 " pdb=" C PRO E 443 " ideal model delta sigma weight residual 110.70 115.50 -4.80 1.22e+00 6.72e-01 1.55e+01 angle pdb=" N PRO B 443 " pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 110.70 115.48 -4.78 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N PRO F 443 " pdb=" CA PRO F 443 " pdb=" C PRO F 443 " ideal model delta sigma weight residual 110.70 115.47 -4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" CA PRO C 443 " pdb=" C PRO C 443 " pdb=" N PRO C 444 " ideal model delta sigma weight residual 117.93 122.62 -4.69 1.20e+00 6.94e-01 1.53e+01 angle pdb=" N PRO A 443 " pdb=" CA PRO A 443 " pdb=" C PRO A 443 " ideal model delta sigma weight residual 110.70 115.46 -4.76 1.22e+00 6.72e-01 1.52e+01 ... (remaining 44917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 18249 17.44 - 34.89: 1149 34.89 - 52.33: 258 52.33 - 69.77: 162 69.77 - 87.22: 30 Dihedral angle restraints: 19848 sinusoidal: 8304 harmonic: 11544 Sorted by residual: dihedral pdb=" C ILE D 390 " pdb=" N ILE D 390 " pdb=" CA ILE D 390 " pdb=" CB ILE D 390 " ideal model delta harmonic sigma weight residual -122.00 -131.59 9.59 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C ILE F 390 " pdb=" N ILE F 390 " pdb=" CA ILE F 390 " pdb=" CB ILE F 390 " ideal model delta harmonic sigma weight residual -122.00 -131.58 9.58 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C ILE C 390 " pdb=" N ILE C 390 " pdb=" CA ILE C 390 " pdb=" CB ILE C 390 " ideal model delta harmonic sigma weight residual -122.00 -131.58 9.58 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 19845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3993 0.063 - 0.125: 701 0.125 - 0.188: 70 0.188 - 0.250: 18 0.250 - 0.313: 12 Chirality restraints: 4794 Sorted by residual: chirality pdb=" CB ILE E 390 " pdb=" CA ILE E 390 " pdb=" CG1 ILE E 390 " pdb=" CG2 ILE E 390 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE C 390 " pdb=" CA ILE C 390 " pdb=" CG1 ILE C 390 " pdb=" CG2 ILE C 390 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE B 390 " pdb=" CA ILE B 390 " pdb=" CG1 ILE B 390 " pdb=" CG2 ILE B 390 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4791 not shown) Planarity restraints: 5844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N ZR5 B 902 " -0.127 2.00e-02 2.50e+03 8.63e-02 1.49e+02 pdb=" C10 ZR5 B 902 " 0.078 2.00e-02 2.50e+03 pdb=" C11 ZR5 B 902 " 0.060 2.00e-02 2.50e+03 pdb=" C12 ZR5 B 902 " 0.076 2.00e-02 2.50e+03 pdb=" C13 ZR5 B 902 " 0.039 2.00e-02 2.50e+03 pdb=" C8 ZR5 B 902 " -0.005 2.00e-02 2.50e+03 pdb=" C9 ZR5 B 902 " 0.037 2.00e-02 2.50e+03 pdb=" S ZR5 B 902 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N ZR5 C 902 " -0.128 2.00e-02 2.50e+03 8.63e-02 1.49e+02 pdb=" C10 ZR5 C 902 " 0.078 2.00e-02 2.50e+03 pdb=" C11 ZR5 C 902 " 0.059 2.00e-02 2.50e+03 pdb=" C12 ZR5 C 902 " 0.075 2.00e-02 2.50e+03 pdb=" C13 ZR5 C 902 " 0.041 2.00e-02 2.50e+03 pdb=" C8 ZR5 C 902 " -0.004 2.00e-02 2.50e+03 pdb=" C9 ZR5 C 902 " 0.038 2.00e-02 2.50e+03 pdb=" S ZR5 C 902 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N ZR5 F 902 " -0.126 2.00e-02 2.50e+03 8.57e-02 1.47e+02 pdb=" C10 ZR5 F 902 " 0.077 2.00e-02 2.50e+03 pdb=" C11 ZR5 F 902 " 0.059 2.00e-02 2.50e+03 pdb=" C12 ZR5 F 902 " 0.075 2.00e-02 2.50e+03 pdb=" C13 ZR5 F 902 " 0.040 2.00e-02 2.50e+03 pdb=" C8 ZR5 F 902 " -0.005 2.00e-02 2.50e+03 pdb=" C9 ZR5 F 902 " 0.037 2.00e-02 2.50e+03 pdb=" S ZR5 F 902 " -0.157 2.00e-02 2.50e+03 ... (remaining 5841 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1503 2.73 - 3.27: 31723 3.27 - 3.82: 60581 3.82 - 4.36: 74506 4.36 - 4.90: 121518 Nonbonded interactions: 289831 Sorted by model distance: nonbonded pdb=" NE2 HIS D 365 " pdb="FE FE2 D 901 " model vdw 2.189 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.191 3.080 nonbonded pdb=" NE2 HIS F 365 " pdb="FE FE2 F 901 " model vdw 2.191 3.080 nonbonded pdb=" NE2 HIS C 365 " pdb="FE FE2 C 901 " model vdw 2.199 3.080 nonbonded pdb=" OXT ILE A 663 " pdb="FE FE2 A 901 " model vdw 2.199 3.000 ... (remaining 289826 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 32.310 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 : 0.005 0.076 33072 Z= 0.223 Angle : 0.843 10.025 44922 Z= 0.447 Chirality : 0.051 0.313 4794 Planarity : 0.010 0.129 5844 Dihedral : 14.059 87.218 12372 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.12), residues: 3960 helix: 0.68 (0.11), residues: 1770 sheet: -0.16 (0.23), residues: 438 loop : 0.18 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG F 98 TYR 0.018 0.003 TYR E 474 PHE 0.016 0.003 PHE C 228 TRP 0.016 0.002 TRP C 208 HIS 0.009 0.002 HIS F 609 Details of bonding type rmsd covalent geometry : bond 0.00505 (33072) covalent geometry : angle 0.84296 (44922) hydrogen bonds : bond 0.13382 ( 1620) hydrogen bonds : angle 6.89246 ( 4533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASN cc_start: 0.7891 (m110) cc_final: 0.7669 (m-40) REVERT: A 21 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7096 (mtt-85) REVERT: A 34 GLU cc_start: 0.8172 (tt0) cc_final: 0.7903 (tm-30) REVERT: A 156 ARG cc_start: 0.7471 (mtm110) cc_final: 0.7031 (mmt-90) REVERT: A 159 ASP cc_start: 0.8527 (m-30) cc_final: 0.8322 (m-30) REVERT: A 611 LYS cc_start: 0.8604 (mmpt) cc_final: 0.8403 (mmtp) REVERT: B 3 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7485 (tmm-80) REVERT: B 20 ASN cc_start: 0.7916 (m110) cc_final: 0.7638 (m-40) REVERT: B 21 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7237 (mtt-85) REVERT: B 34 GLU cc_start: 0.8199 (tt0) cc_final: 0.7939 (tm-30) REVERT: B 35 LEU cc_start: 0.8270 (mp) cc_final: 0.8014 (mp) REVERT: B 51 HIS cc_start: 0.7162 (t-90) cc_final: 0.6953 (t-90) REVERT: B 156 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7282 (mmt-90) REVERT: B 175 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7890 (mm-30) REVERT: B 239 MET cc_start: 0.8984 (mmm) cc_final: 0.8681 (mmm) REVERT: B 263 GLN cc_start: 0.8609 (mt0) cc_final: 0.8408 (mt0) REVERT: B 591 MET cc_start: 0.9212 (mtp) cc_final: 0.8941 (mtp) REVERT: C 20 ASN cc_start: 0.7857 (m110) cc_final: 0.7654 (m-40) REVERT: C 21 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7243 (mtt-85) REVERT: C 34 GLU cc_start: 0.8161 (tt0) cc_final: 0.7942 (tm-30) REVERT: C 51 HIS cc_start: 0.7148 (t-90) cc_final: 0.6939 (t-90) REVERT: C 156 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7261 (mmt-90) REVERT: C 175 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7895 (mm-30) REVERT: C 239 MET cc_start: 0.9002 (mmm) cc_final: 0.8598 (mmm) REVERT: C 591 MET cc_start: 0.9185 (mtp) cc_final: 0.8893 (mtp) REVERT: D 21 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7206 (mtt-85) REVERT: D 34 GLU cc_start: 0.8180 (tt0) cc_final: 0.7859 (tm-30) REVERT: D 156 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6880 (mmp80) REVERT: D 171 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8151 (ttp-110) REVERT: D 239 MET cc_start: 0.8948 (mmm) cc_final: 0.8596 (mmm) REVERT: D 376 MET cc_start: 0.9261 (mmm) cc_final: 0.9007 (mmm) REVERT: D 571 ASP cc_start: 0.7632 (m-30) cc_final: 0.7379 (m-30) REVERT: D 574 MET cc_start: 0.9053 (tpp) cc_final: 0.8838 (tpp) REVERT: D 632 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7548 (tp30) REVERT: E 5 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.6990 (ttp-170) REVERT: E 20 ASN cc_start: 0.7973 (m110) cc_final: 0.7522 (m-40) REVERT: E 21 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7207 (mtt-85) REVERT: E 34 GLU cc_start: 0.8148 (tt0) cc_final: 0.7909 (tm-30) REVERT: E 156 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7214 (mmt-90) REVERT: E 159 ASP cc_start: 0.8472 (m-30) cc_final: 0.8237 (m-30) REVERT: E 175 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7982 (mm-30) REVERT: E 239 MET cc_start: 0.9038 (mmm) cc_final: 0.8739 (mmm) REVERT: F 4 TYR cc_start: 0.8517 (m-80) cc_final: 0.8177 (m-80) REVERT: F 5 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.6869 (ttp-170) REVERT: F 20 ASN cc_start: 0.7919 (m110) cc_final: 0.7714 (m-40) REVERT: F 156 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7339 (mmt-90) REVERT: F 159 ASP cc_start: 0.8545 (m-30) cc_final: 0.8300 (m-30) REVERT: F 239 MET cc_start: 0.9016 (mmm) cc_final: 0.8810 (mmm) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 0.9694 time to fit residues: 635.4876 Evaluate side-chains 437 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 84 GLN B 270 ASN B 625 ASN C 263 GLN C 270 ASN D 20 ASN D 263 GLN D 270 ASN D 400 ASN E 263 GLN E 270 ASN E 596 HIS F 270 ASN F 400 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.091807 restraints weight = 36514.741| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.88 r_work: 0.3109 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 33072 Z= 0.250 Angle : 0.611 8.832 44922 Z= 0.314 Chirality : 0.045 0.222 4794 Planarity : 0.006 0.083 5844 Dihedral : 6.690 59.585 4494 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 7.91 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.13), residues: 3960 helix: 1.30 (0.12), residues: 1806 sheet: -0.35 (0.22), residues: 444 loop : 0.49 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 5 TYR 0.022 0.002 TYR B 97 PHE 0.023 0.002 PHE E 386 TRP 0.011 0.002 TRP F 346 HIS 0.005 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00568 (33072) covalent geometry : angle 0.61098 (44922) hydrogen bonds : bond 0.05077 ( 1620) hydrogen bonds : angle 5.56884 ( 4533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 444 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7307 (tmm-80) REVERT: A 21 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7319 (mtt-85) REVERT: A 45 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 156 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7198 (mmt-90) REVERT: A 611 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8578 (mmtp) REVERT: A 650 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8276 (mm-30) REVERT: A 653 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8245 (mtmp) REVERT: B 3 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7491 (tmm-80) REVERT: B 21 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7424 (mtt-85) REVERT: B 156 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7356 (mmt-90) REVERT: B 175 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8051 (mm-30) REVERT: B 239 MET cc_start: 0.9260 (mmm) cc_final: 0.8976 (mmm) REVERT: B 259 GLU cc_start: 0.8321 (tt0) cc_final: 0.7838 (pm20) REVERT: B 591 MET cc_start: 0.9180 (mtp) cc_final: 0.8922 (mtp) REVERT: C 3 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.7462 (tmm-80) REVERT: C 21 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7408 (mtt-85) REVERT: C 51 HIS cc_start: 0.7511 (t-90) cc_final: 0.7250 (t-90) REVERT: C 138 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8541 (pt) REVERT: C 156 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7416 (mmt-90) REVERT: C 175 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7971 (mm-30) REVERT: C 239 MET cc_start: 0.9274 (mmm) cc_final: 0.9011 (mmm) REVERT: C 591 MET cc_start: 0.9188 (mtp) cc_final: 0.8877 (mtp) REVERT: C 633 LYS cc_start: 0.8758 (tttt) cc_final: 0.8545 (tttm) REVERT: D 3 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7425 (tmm-80) REVERT: D 21 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7502 (mtt-85) REVERT: D 45 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 131 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: D 156 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7217 (mmp80) REVERT: D 571 ASP cc_start: 0.7983 (m-30) cc_final: 0.7714 (m-30) REVERT: D 632 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7802 (tp30) REVERT: D 650 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: E 3 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7657 (tmm160) REVERT: E 5 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7672 (tpp80) REVERT: E 21 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7530 (mtt-85) REVERT: E 48 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7677 (tt0) REVERT: E 68 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7132 (t70) REVERT: E 138 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8570 (pt) REVERT: E 156 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7170 (mmt-90) REVERT: E 159 ASP cc_start: 0.8749 (m-30) cc_final: 0.8432 (m-30) REVERT: E 239 MET cc_start: 0.9216 (mmm) cc_final: 0.8821 (mmm) REVERT: E 259 GLU cc_start: 0.8410 (tt0) cc_final: 0.7844 (pm20) REVERT: E 270 ASN cc_start: 0.8857 (t0) cc_final: 0.8656 (t0) REVERT: F 3 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7353 (tmm-80) REVERT: F 20 ASN cc_start: 0.8469 (m110) cc_final: 0.8100 (m-40) REVERT: F 21 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7789 (mtt-85) REVERT: F 156 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7151 (mmt-90) REVERT: F 159 ASP cc_start: 0.8774 (m-30) cc_final: 0.8488 (m-30) REVERT: F 239 MET cc_start: 0.9248 (mmm) cc_final: 0.9048 (mmm) REVERT: F 650 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: F 653 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8168 (mtmp) outliers start: 39 outliers final: 13 residues processed: 469 average time/residue: 0.8588 time to fit residues: 461.4457 Evaluate side-chains 431 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 409 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 68 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 296 optimal weight: 0.0170 chunk 186 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 263 GLN A 400 ASN B 263 GLN B 270 ASN B 625 ASN C 84 GLN C 263 GLN C 270 ASN D 38 GLN D 51 HIS D 198 ASN D 263 GLN D 270 ASN D 625 ASN E 38 GLN E 263 GLN F 198 ASN F 263 GLN F 270 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.092261 restraints weight = 36276.462| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.86 r_work: 0.3117 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33072 Z= 0.203 Angle : 0.564 9.282 44922 Z= 0.289 Chirality : 0.043 0.238 4794 Planarity : 0.005 0.093 5844 Dihedral : 6.515 55.790 4494 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.81 % Allowed : 8.87 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.13), residues: 3960 helix: 1.33 (0.12), residues: 1830 sheet: -0.69 (0.21), residues: 474 loop : 0.63 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 5 TYR 0.017 0.002 TYR F 460 PHE 0.015 0.002 PHE B 482 TRP 0.011 0.002 TRP A 208 HIS 0.005 0.001 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00459 (33072) covalent geometry : angle 0.56427 (44922) hydrogen bonds : bond 0.04733 ( 1620) hydrogen bonds : angle 5.42226 ( 4533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 429 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7301 (tmm-80) REVERT: A 21 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7356 (mtt-85) REVERT: A 156 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7225 (mmp80) REVERT: A 611 LYS cc_start: 0.8923 (mmpt) cc_final: 0.8596 (mmtp) REVERT: A 650 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8639 (mm-30) REVERT: A 653 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8320 (mtmp) REVERT: B 3 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7439 (tmm-80) REVERT: B 21 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7447 (mtt-85) REVERT: B 156 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7392 (mmt-90) REVERT: B 175 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8059 (mm-30) REVERT: B 239 MET cc_start: 0.9207 (mmm) cc_final: 0.8915 (mmm) REVERT: B 259 GLU cc_start: 0.8324 (tt0) cc_final: 0.7847 (pm20) REVERT: B 591 MET cc_start: 0.9186 (mtp) cc_final: 0.8972 (mtp) REVERT: C 3 ARG cc_start: 0.7753 (tpp-160) cc_final: 0.7375 (tmm-80) REVERT: C 21 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7352 (mtt-85) REVERT: C 45 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 51 HIS cc_start: 0.7543 (t-90) cc_final: 0.7322 (t-90) REVERT: C 138 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8576 (pt) REVERT: C 156 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7335 (mmp80) REVERT: C 175 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7955 (mm-30) REVERT: C 239 MET cc_start: 0.9231 (mmm) cc_final: 0.8946 (mmm) REVERT: C 571 ASP cc_start: 0.8002 (m-30) cc_final: 0.7770 (m-30) REVERT: C 591 MET cc_start: 0.9182 (mtp) cc_final: 0.8845 (mtp) REVERT: C 633 LYS cc_start: 0.8712 (tttt) cc_final: 0.8478 (tttm) REVERT: D 3 ARG cc_start: 0.7888 (tpp-160) cc_final: 0.7388 (tmm-80) REVERT: D 21 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7423 (mtt-85) REVERT: D 45 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7584 (mt-10) REVERT: D 66 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8244 (ttm-80) REVERT: D 156 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7195 (mmp80) REVERT: D 571 ASP cc_start: 0.7994 (m-30) cc_final: 0.7712 (m-30) REVERT: D 632 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7763 (tp30) REVERT: D 650 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: E 3 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7593 (tmm160) REVERT: E 21 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7456 (mtt-85) REVERT: E 48 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7824 (tp30) REVERT: E 68 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7056 (t70) REVERT: E 138 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8523 (pt) REVERT: E 156 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7226 (mmt-90) REVERT: E 159 ASP cc_start: 0.8756 (m-30) cc_final: 0.8445 (m-30) REVERT: E 239 MET cc_start: 0.9186 (mmm) cc_final: 0.8812 (mmm) REVERT: E 259 GLU cc_start: 0.8443 (tt0) cc_final: 0.7843 (pm20) REVERT: E 270 ASN cc_start: 0.8895 (t0) cc_final: 0.8646 (t0) REVERT: E 650 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: F 21 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7698 (mtt-85) REVERT: F 156 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7171 (mmt-90) REVERT: F 159 ASP cc_start: 0.8775 (m-30) cc_final: 0.8510 (m-30) REVERT: F 650 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8192 (mm-30) REVERT: F 653 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8164 (mtmp) outliers start: 62 outliers final: 23 residues processed: 466 average time/residue: 0.7793 time to fit residues: 416.4419 Evaluate side-chains 443 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 410 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 68 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 650 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 305 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 20 ASN B 84 GLN B 263 GLN B 270 ASN C 263 GLN C 270 ASN D 38 GLN D 198 ASN D 263 GLN E 84 GLN E 263 GLN F 198 ASN F 263 GLN F 270 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093409 restraints weight = 35977.704| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.85 r_work: 0.3136 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33072 Z= 0.170 Angle : 0.537 7.773 44922 Z= 0.275 Chirality : 0.041 0.240 4794 Planarity : 0.005 0.101 5844 Dihedral : 6.369 55.978 4494 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.72 % Allowed : 10.04 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.13), residues: 3960 helix: 1.43 (0.12), residues: 1830 sheet: -0.75 (0.21), residues: 474 loop : 0.69 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 5 TYR 0.017 0.002 TYR F 460 PHE 0.012 0.002 PHE B 482 TRP 0.011 0.001 TRP A 208 HIS 0.006 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00383 (33072) covalent geometry : angle 0.53704 (44922) hydrogen bonds : bond 0.04422 ( 1620) hydrogen bonds : angle 5.30031 ( 4533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 430 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7386 (tmm-80) REVERT: A 21 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7297 (mtt-85) REVERT: A 156 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7259 (mmp80) REVERT: A 611 LYS cc_start: 0.8910 (mmpt) cc_final: 0.8558 (mmtm) REVERT: A 653 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8279 (mtmp) REVERT: B 3 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7486 (tmm-80) REVERT: B 21 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7384 (mtt-85) REVERT: B 156 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7367 (mmt-90) REVERT: B 175 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8041 (mm-30) REVERT: B 239 MET cc_start: 0.9211 (mmm) cc_final: 0.8954 (mmm) REVERT: B 259 GLU cc_start: 0.8296 (tt0) cc_final: 0.7847 (pm20) REVERT: B 653 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8363 (mtmm) REVERT: C 3 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7366 (tmm-80) REVERT: C 21 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7312 (mtt-85) REVERT: C 45 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7444 (mt-10) REVERT: C 51 HIS cc_start: 0.7482 (t-90) cc_final: 0.7260 (t-90) REVERT: C 138 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8590 (pt) REVERT: C 156 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7395 (mmt-90) REVERT: C 175 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7975 (mm-30) REVERT: C 239 MET cc_start: 0.9224 (mmm) cc_final: 0.8981 (mmm) REVERT: C 591 MET cc_start: 0.9181 (mtp) cc_final: 0.8933 (mtp) REVERT: C 635 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: C 653 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: D 3 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7481 (tmm-80) REVERT: D 21 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7462 (mtt-85) REVERT: D 66 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7670 (ttm-80) REVERT: D 131 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: D 156 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7220 (mmp80) REVERT: D 571 ASP cc_start: 0.7993 (m-30) cc_final: 0.7714 (m-30) REVERT: D 632 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7778 (tp30) REVERT: D 650 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: E 3 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7620 (tmm160) REVERT: E 21 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7300 (mtt-85) REVERT: E 66 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8230 (ttm-80) REVERT: E 138 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8618 (pt) REVERT: E 156 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7212 (mmt-90) REVERT: E 159 ASP cc_start: 0.8739 (m-30) cc_final: 0.8430 (m-30) REVERT: E 239 MET cc_start: 0.9177 (mmm) cc_final: 0.8822 (mmm) REVERT: E 270 ASN cc_start: 0.8901 (t0) cc_final: 0.8634 (t0) REVERT: E 650 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: F 3 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7253 (tmm-80) REVERT: F 21 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7529 (mtt-85) REVERT: F 156 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7090 (mmt-90) REVERT: F 159 ASP cc_start: 0.8764 (m-30) cc_final: 0.8495 (m-30) REVERT: F 568 THR cc_start: 0.9021 (p) cc_final: 0.8752 (p) REVERT: F 611 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8546 (mmtm) REVERT: F 650 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: F 653 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8132 (mtmp) outliers start: 59 outliers final: 25 residues processed: 467 average time/residue: 0.8088 time to fit residues: 432.6938 Evaluate side-chains 452 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 414 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 650 GLU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 291 optimal weight: 4.9990 chunk 384 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 305 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 GLN B 20 ASN B 84 GLN B 263 GLN B 270 ASN B 625 ASN C 84 GLN C 270 ASN D 38 GLN D 84 GLN D 198 ASN D 263 GLN D 484 GLN E 38 GLN E 84 GLN E 198 ASN F 198 ASN F 270 ASN F 484 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091100 restraints weight = 36106.621| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.85 r_work: 0.3100 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 33072 Z= 0.244 Angle : 0.586 7.535 44922 Z= 0.299 Chirality : 0.044 0.228 4794 Planarity : 0.006 0.102 5844 Dihedral : 6.534 54.008 4494 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.93 % Allowed : 10.33 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.13), residues: 3960 helix: 1.43 (0.12), residues: 1806 sheet: -0.73 (0.21), residues: 474 loop : 0.68 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 5 TYR 0.019 0.002 TYR D 97 PHE 0.016 0.002 PHE E 386 TRP 0.012 0.002 TRP A 208 HIS 0.008 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00552 (33072) covalent geometry : angle 0.58565 (44922) hydrogen bonds : bond 0.04870 ( 1620) hydrogen bonds : angle 5.38658 ( 4533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7394 (tmm-80) REVERT: A 21 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7436 (mtt-85) REVERT: A 119 ASN cc_start: 0.8956 (t0) cc_final: 0.8704 (t0) REVERT: A 156 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7286 (mmp80) REVERT: A 611 LYS cc_start: 0.8923 (mmpt) cc_final: 0.8563 (mmtm) REVERT: A 653 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8366 (mtmp) REVERT: B 3 ARG cc_start: 0.7804 (tpp-160) cc_final: 0.7513 (ttp-170) REVERT: B 21 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7443 (mtt-85) REVERT: B 156 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7346 (mmt-90) REVERT: B 259 GLU cc_start: 0.8279 (tt0) cc_final: 0.7781 (pm20) REVERT: B 653 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8368 (mtmm) REVERT: C 3 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.7366 (tmm-80) REVERT: C 21 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7322 (mtt-85) REVERT: C 51 HIS cc_start: 0.7446 (t-90) cc_final: 0.7209 (t-90) REVERT: C 138 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8609 (pt) REVERT: C 156 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7276 (mmp80) REVERT: C 568 THR cc_start: 0.9143 (p) cc_final: 0.8878 (p) REVERT: C 591 MET cc_start: 0.9185 (mtp) cc_final: 0.8842 (mtp) REVERT: C 635 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: C 653 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8440 (mtmm) REVERT: D 3 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7517 (tmm-80) REVERT: D 21 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7459 (mtt-85) REVERT: D 131 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: D 156 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7197 (mmp80) REVERT: D 308 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8494 (p0) REVERT: D 632 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7755 (tp30) REVERT: D 650 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: E 21 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7306 (mtt-85) REVERT: E 66 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8202 (ttm-80) REVERT: E 138 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8547 (pt) REVERT: E 156 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7201 (mmt-90) REVERT: E 159 ASP cc_start: 0.8740 (m-30) cc_final: 0.8435 (m-30) REVERT: E 239 MET cc_start: 0.9263 (mmm) cc_final: 0.9015 (mmm) REVERT: E 270 ASN cc_start: 0.8897 (t0) cc_final: 0.8615 (t0) REVERT: E 650 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: F 21 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7733 (mtt-85) REVERT: F 156 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7121 (mmt-90) REVERT: F 159 ASP cc_start: 0.8785 (m-30) cc_final: 0.8543 (m-30) REVERT: F 568 THR cc_start: 0.9057 (p) cc_final: 0.8811 (p) REVERT: F 650 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: F 653 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8167 (mtmp) outliers start: 66 outliers final: 27 residues processed: 462 average time/residue: 0.8767 time to fit residues: 462.3102 Evaluate side-chains 435 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 395 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 650 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 143 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 246 optimal weight: 0.3980 chunk 233 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 263 GLN B 270 ASN B 625 ASN C 84 GLN C 263 GLN C 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 198 ASN E 263 GLN F 198 ASN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094663 restraints weight = 35036.792| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.82 r_work: 0.3156 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33072 Z= 0.143 Angle : 0.520 10.083 44922 Z= 0.266 Chirality : 0.040 0.212 4794 Planarity : 0.005 0.106 5844 Dihedral : 6.300 57.745 4494 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.75 % Allowed : 11.47 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.13), residues: 3960 helix: 1.49 (0.12), residues: 1830 sheet: -0.84 (0.20), residues: 474 loop : 0.71 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 7 TYR 0.016 0.002 TYR F 460 PHE 0.011 0.001 PHE B 482 TRP 0.010 0.001 TRP C 176 HIS 0.006 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00321 (33072) covalent geometry : angle 0.52041 (44922) hydrogen bonds : bond 0.04177 ( 1620) hydrogen bonds : angle 5.22582 ( 4533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 429 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7382 (tmm-80) REVERT: A 21 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7290 (mtt-85) REVERT: A 156 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7299 (mmt-90) REVERT: A 611 LYS cc_start: 0.8893 (mmpt) cc_final: 0.8542 (mmtm) REVERT: A 653 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8271 (mtmp) REVERT: B 3 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7492 (tmm-80) REVERT: B 21 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7360 (mtt-85) REVERT: B 156 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7351 (mmt-90) REVERT: B 175 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8033 (mm-30) REVERT: B 259 GLU cc_start: 0.8242 (tt0) cc_final: 0.7796 (pm20) REVERT: B 653 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8279 (mtmm) REVERT: C 3 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7415 (tmm-80) REVERT: C 21 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7300 (mtt-85) REVERT: C 45 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7470 (mt-10) REVERT: C 51 HIS cc_start: 0.7122 (t-90) cc_final: 0.6886 (t-90) REVERT: C 138 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8583 (pt) REVERT: C 156 ARG cc_start: 0.7997 (mtm110) cc_final: 0.7246 (mmp80) REVERT: C 568 THR cc_start: 0.9127 (p) cc_final: 0.8882 (p) REVERT: C 635 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: C 653 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8368 (mtmm) REVERT: D 3 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7517 (tmm-80) REVERT: D 5 ARG cc_start: 0.8281 (ttt90) cc_final: 0.7904 (tpp80) REVERT: D 21 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7459 (mtt-85) REVERT: D 66 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: D 131 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: D 156 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7172 (mmp80) REVERT: D 650 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8043 (mm-30) REVERT: D 653 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8029 (mtmp) REVERT: E 21 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7293 (mtt-85) REVERT: E 48 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: E 66 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8188 (ttm-80) REVERT: E 138 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8458 (pp) REVERT: E 156 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7207 (mmt-90) REVERT: E 159 ASP cc_start: 0.8722 (m-30) cc_final: 0.8428 (m-30) REVERT: E 239 MET cc_start: 0.9157 (mmm) cc_final: 0.8938 (mmm) REVERT: E 270 ASN cc_start: 0.8897 (t0) cc_final: 0.8639 (t0) REVERT: F 45 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7587 (mt-10) REVERT: F 48 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7470 (mm-30) REVERT: F 156 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7106 (mmt-90) REVERT: F 159 ASP cc_start: 0.8755 (m-30) cc_final: 0.8495 (m-30) REVERT: F 249 SER cc_start: 0.9074 (m) cc_final: 0.8735 (p) REVERT: F 476 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: F 568 THR cc_start: 0.9020 (p) cc_final: 0.8761 (p) REVERT: F 650 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: F 653 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8098 (mtmp) outliers start: 60 outliers final: 24 residues processed: 469 average time/residue: 0.7673 time to fit residues: 413.0076 Evaluate side-chains 443 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 404 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 613 LYS Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 394 optimal weight: 4.9990 chunk 50 optimal weight: 0.0030 chunk 262 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN B 484 GLN C 84 GLN C 263 GLN C 270 ASN C 484 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 84 GLN E 198 ASN E 263 GLN F 68 HIS F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093481 restraints weight = 35302.972| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.83 r_work: 0.3139 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33072 Z= 0.176 Angle : 0.540 8.819 44922 Z= 0.276 Chirality : 0.041 0.202 4794 Planarity : 0.005 0.113 5844 Dihedral : 6.362 59.861 4494 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.46 % Allowed : 12.03 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.13), residues: 3960 helix: 1.50 (0.12), residues: 1830 sheet: -0.79 (0.20), residues: 474 loop : 0.72 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 7 TYR 0.017 0.002 TYR E 460 PHE 0.012 0.002 PHE D 386 TRP 0.010 0.001 TRP A 208 HIS 0.006 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00399 (33072) covalent geometry : angle 0.54031 (44922) hydrogen bonds : bond 0.04369 ( 1620) hydrogen bonds : angle 5.22814 ( 4533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 417 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7382 (tmm-80) REVERT: A 21 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7303 (mtt-85) REVERT: A 156 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7301 (mmt-90) REVERT: A 611 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8557 (mmtm) REVERT: A 653 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8263 (mtmp) REVERT: B 3 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7499 (tmm-80) REVERT: B 21 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7377 (mtt-85) REVERT: B 156 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7368 (mmt-90) REVERT: B 259 GLU cc_start: 0.8244 (tt0) cc_final: 0.7774 (pm20) REVERT: B 653 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8358 (mtmm) REVERT: C 3 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7466 (tmm-80) REVERT: C 21 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7315 (mtt-85) REVERT: C 45 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7405 (mt-10) REVERT: C 156 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7265 (mmp80) REVERT: C 568 THR cc_start: 0.9119 (p) cc_final: 0.8868 (p) REVERT: C 635 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: C 653 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8396 (mtmm) REVERT: D 3 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.7534 (tmm-80) REVERT: D 5 ARG cc_start: 0.8308 (ttt90) cc_final: 0.7920 (tpp80) REVERT: D 21 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7486 (mtt-85) REVERT: D 66 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8040 (ttm-80) REVERT: D 131 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: D 156 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7188 (mmp80) REVERT: D 650 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: D 653 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7977 (mtmp) REVERT: E 21 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7278 (mtt-85) REVERT: E 48 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: E 66 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: E 138 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8466 (pp) REVERT: E 156 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7204 (mmt-90) REVERT: E 159 ASP cc_start: 0.8732 (m-30) cc_final: 0.8436 (m-30) REVERT: E 239 MET cc_start: 0.9198 (mmm) cc_final: 0.8963 (mmm) REVERT: E 270 ASN cc_start: 0.8904 (t0) cc_final: 0.8633 (t0) REVERT: F 45 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7592 (mt-10) REVERT: F 48 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7479 (mm-30) REVERT: F 156 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7074 (mmp80) REVERT: F 159 ASP cc_start: 0.8766 (m-30) cc_final: 0.8506 (m-30) REVERT: F 568 THR cc_start: 0.9028 (p) cc_final: 0.8775 (p) REVERT: F 650 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: F 653 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8111 (mtmp) outliers start: 50 outliers final: 25 residues processed: 449 average time/residue: 0.8533 time to fit residues: 437.8141 Evaluate side-chains 439 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 401 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 613 LYS Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 613 LYS Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 202 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 333 optimal weight: 10.0000 chunk 265 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN C 263 GLN C 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN F 68 HIS F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094700 restraints weight = 35003.283| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.82 r_work: 0.3158 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33072 Z= 0.149 Angle : 0.523 7.874 44922 Z= 0.268 Chirality : 0.041 0.207 4794 Planarity : 0.005 0.095 5844 Dihedral : 6.245 58.608 4494 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.43 % Allowed : 12.14 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 3960 helix: 1.54 (0.12), residues: 1830 sheet: -0.81 (0.20), residues: 474 loop : 0.72 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 7 TYR 0.016 0.002 TYR F 460 PHE 0.010 0.001 PHE B 482 TRP 0.009 0.001 TRP A 208 HIS 0.007 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00335 (33072) covalent geometry : angle 0.52259 (44922) hydrogen bonds : bond 0.04171 ( 1620) hydrogen bonds : angle 5.17915 ( 4533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 422 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7380 (tmm-80) REVERT: A 21 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7282 (mtt-85) REVERT: A 156 ARG cc_start: 0.8049 (mtm110) cc_final: 0.7310 (mmt-90) REVERT: A 611 LYS cc_start: 0.8902 (mmpt) cc_final: 0.8555 (mmtm) REVERT: A 653 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8232 (mtmp) REVERT: B 3 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7452 (tmm-80) REVERT: B 21 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7342 (mtt-85) REVERT: B 156 ARG cc_start: 0.8085 (mtm110) cc_final: 0.7372 (mmt-90) REVERT: B 259 GLU cc_start: 0.8233 (tt0) cc_final: 0.7769 (pm20) REVERT: B 653 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8337 (mtmm) REVERT: C 3 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7450 (tmm-80) REVERT: C 21 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7300 (mtt-85) REVERT: C 45 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7406 (mt-10) REVERT: C 156 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7284 (mmp80) REVERT: C 568 THR cc_start: 0.9118 (p) cc_final: 0.8877 (p) REVERT: C 635 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: C 653 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: D 3 ARG cc_start: 0.7777 (tpp-160) cc_final: 0.7515 (tmm-80) REVERT: D 5 ARG cc_start: 0.8269 (ttt90) cc_final: 0.7066 (tpp80) REVERT: D 21 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7473 (mtt-85) REVERT: D 66 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7621 (ttm-80) REVERT: D 131 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: D 156 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7210 (mmp80) REVERT: D 650 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8033 (mm-30) REVERT: D 653 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.7958 (mtmp) REVERT: E 21 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7302 (mtt-85) REVERT: E 66 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8163 (ttm-80) REVERT: E 156 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7228 (mmt-90) REVERT: E 159 ASP cc_start: 0.8720 (m-30) cc_final: 0.8446 (m-30) REVERT: E 239 MET cc_start: 0.9175 (mmm) cc_final: 0.8954 (mmm) REVERT: E 270 ASN cc_start: 0.8896 (t0) cc_final: 0.8645 (t0) REVERT: F 45 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7594 (mt-10) REVERT: F 48 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7421 (mm-30) REVERT: F 156 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7078 (mmp80) REVERT: F 159 ASP cc_start: 0.8754 (m-30) cc_final: 0.8497 (m-30) REVERT: F 249 SER cc_start: 0.9068 (m) cc_final: 0.8754 (p) REVERT: F 476 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 568 THR cc_start: 0.9027 (p) cc_final: 0.8767 (p) REVERT: F 650 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: F 653 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8088 (mtmp) outliers start: 49 outliers final: 22 residues processed: 454 average time/residue: 0.7921 time to fit residues: 412.0750 Evaluate side-chains 443 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 409 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 613 LYS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 613 LYS Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 653 LYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 613 LYS Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 161 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 372 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 320 optimal weight: 0.0470 chunk 189 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 351 optimal weight: 0.7980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 270 ASN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN C 263 GLN C 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN F 198 ASN F 263 GLN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096207 restraints weight = 34884.669| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.82 r_work: 0.3150 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33072 Z= 0.125 Angle : 0.511 8.498 44922 Z= 0.261 Chirality : 0.040 0.199 4794 Planarity : 0.005 0.116 5844 Dihedral : 6.029 52.984 4494 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.34 % Allowed : 12.32 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.13), residues: 3960 helix: 1.63 (0.12), residues: 1824 sheet: -0.70 (0.21), residues: 474 loop : 0.74 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 7 TYR 0.017 0.002 TYR A 139 PHE 0.009 0.001 PHE C 174 TRP 0.009 0.001 TRP F 141 HIS 0.005 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00282 (33072) covalent geometry : angle 0.51142 (44922) hydrogen bonds : bond 0.03956 ( 1620) hydrogen bonds : angle 5.09446 ( 4533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7416 (tmm-80) REVERT: A 21 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7251 (mtt-85) REVERT: A 48 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: A 156 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7330 (mmt-90) REVERT: A 611 LYS cc_start: 0.8895 (mmpt) cc_final: 0.8547 (mmtm) REVERT: A 653 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8209 (mtmp) REVERT: B 3 ARG cc_start: 0.7771 (tpp-160) cc_final: 0.7472 (tmm-80) REVERT: B 21 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7328 (mtt-85) REVERT: B 51 HIS cc_start: 0.7160 (m-70) cc_final: 0.6874 (t-90) REVERT: B 156 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7394 (mmt-90) REVERT: B 175 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8005 (mm-30) REVERT: B 259 GLU cc_start: 0.8227 (tt0) cc_final: 0.7764 (pm20) REVERT: B 653 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: C 3 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.7455 (tmm-80) REVERT: C 5 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.7697 (tpp80) REVERT: C 21 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7276 (mtt-85) REVERT: C 45 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 51 HIS cc_start: 0.7144 (m-70) cc_final: 0.6831 (t-90) REVERT: C 156 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7299 (mmp80) REVERT: C 568 THR cc_start: 0.9106 (p) cc_final: 0.8863 (p) REVERT: C 635 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8581 (tt0) REVERT: C 653 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8341 (mtmm) REVERT: D 3 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7505 (tmm-80) REVERT: D 21 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7469 (mtt-85) REVERT: D 131 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: D 156 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7209 (mmp80) REVERT: D 308 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8472 (p0) REVERT: D 476 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: D 650 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8228 (mm-30) REVERT: E 5 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7744 (tpt-90) REVERT: E 21 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7286 (mtt-85) REVERT: E 66 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8149 (ttm-80) REVERT: E 156 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7226 (mmt-90) REVERT: E 159 ASP cc_start: 0.8736 (m-30) cc_final: 0.8472 (m-30) REVERT: E 239 MET cc_start: 0.9172 (mmm) cc_final: 0.8821 (mmm) REVERT: E 270 ASN cc_start: 0.8884 (t0) cc_final: 0.8641 (t0) REVERT: F 3 ARG cc_start: 0.7878 (tpp-160) cc_final: 0.7139 (tmm-80) REVERT: F 45 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7596 (mt-10) REVERT: F 48 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7403 (mm-30) REVERT: F 156 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7085 (mmp80) REVERT: F 159 ASP cc_start: 0.8748 (m-30) cc_final: 0.8491 (m-30) REVERT: F 476 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: F 568 THR cc_start: 0.9012 (p) cc_final: 0.8752 (p) REVERT: F 650 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8198 (mm-30) outliers start: 46 outliers final: 19 residues processed: 455 average time/residue: 0.7888 time to fit residues: 413.0700 Evaluate side-chains 444 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 413 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 377 optimal weight: 8.9990 chunk 98 optimal weight: 0.0000 chunk 280 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 339 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 297 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 361 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN C 263 GLN C 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN E 84 GLN E 198 ASN E 263 GLN F 198 ASN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097898 restraints weight = 35411.547| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.81 r_work: 0.3186 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33072 Z= 0.117 Angle : 0.506 7.959 44922 Z= 0.259 Chirality : 0.040 0.209 4794 Planarity : 0.005 0.114 5844 Dihedral : 5.868 50.825 4494 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.14 % Allowed : 12.78 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.13), residues: 3960 helix: 1.71 (0.12), residues: 1830 sheet: -0.63 (0.21), residues: 474 loop : 0.76 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 7 TYR 0.018 0.002 TYR D 139 PHE 0.009 0.001 PHE C 174 TRP 0.010 0.001 TRP A 498 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00263 (33072) covalent geometry : angle 0.50555 (44922) hydrogen bonds : bond 0.03850 ( 1620) hydrogen bonds : angle 5.03442 ( 4533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 428 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7454 (tmm-80) REVERT: A 5 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7886 (ttt180) REVERT: A 21 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7295 (mtt-85) REVERT: A 48 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 156 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7338 (mmt-90) REVERT: A 611 LYS cc_start: 0.8893 (mmpt) cc_final: 0.8551 (mmtm) REVERT: A 653 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8249 (mtmp) REVERT: B 3 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7522 (tmm-80) REVERT: B 21 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7301 (mtt-85) REVERT: B 51 HIS cc_start: 0.7266 (m-70) cc_final: 0.6984 (t-90) REVERT: B 156 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7417 (mmt-90) REVERT: B 175 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8020 (mm-30) REVERT: B 259 GLU cc_start: 0.8221 (tt0) cc_final: 0.7790 (pm20) REVERT: B 653 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8274 (mtmm) REVERT: C 3 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7534 (tmm-80) REVERT: C 5 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7790 (tpp80) REVERT: C 21 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7303 (mtt-85) REVERT: C 45 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 51 HIS cc_start: 0.7205 (m-70) cc_final: 0.6948 (t-90) REVERT: C 156 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7315 (mmp80) REVERT: C 270 ASN cc_start: 0.8913 (t0) cc_final: 0.8612 (t0) REVERT: C 561 MET cc_start: 0.8933 (mmm) cc_final: 0.8614 (mmt) REVERT: C 568 THR cc_start: 0.9124 (p) cc_final: 0.8884 (p) REVERT: C 635 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: C 653 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: D 3 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7508 (tmm-80) REVERT: D 21 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7436 (mtt-85) REVERT: D 156 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7238 (mmp80) REVERT: D 308 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8477 (p0) REVERT: D 476 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: D 650 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: E 5 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7780 (tpt-90) REVERT: E 21 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7293 (mtt-85) REVERT: E 66 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8160 (ttm-80) REVERT: E 156 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7278 (mmt-90) REVERT: E 159 ASP cc_start: 0.8745 (m-30) cc_final: 0.8481 (m-30) REVERT: E 239 MET cc_start: 0.9184 (mmm) cc_final: 0.8849 (mmm) REVERT: E 270 ASN cc_start: 0.8896 (t0) cc_final: 0.8656 (t0) REVERT: F 45 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7593 (mt-10) REVERT: F 48 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7443 (mm-30) REVERT: F 156 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7086 (mmp80) REVERT: F 159 ASP cc_start: 0.8759 (m-30) cc_final: 0.8490 (m-30) REVERT: F 249 SER cc_start: 0.9094 (m) cc_final: 0.8790 (p) REVERT: F 476 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: F 568 THR cc_start: 0.9016 (p) cc_final: 0.8759 (p) REVERT: F 650 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: F 653 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8050 (mtmp) outliers start: 39 outliers final: 17 residues processed: 453 average time/residue: 0.8417 time to fit residues: 438.2368 Evaluate side-chains 448 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 420 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 439 CYS Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 650 GLU Chi-restraints excluded: chain F residue 653 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 284 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 239 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 361 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 198 ASN F 198 ASN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095006 restraints weight = 34868.747| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.82 r_work: 0.3161 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33072 Z= 0.157 Angle : 0.533 7.982 44922 Z= 0.272 Chirality : 0.041 0.211 4794 Planarity : 0.005 0.091 5844 Dihedral : 5.874 48.046 4494 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.99 % Allowed : 13.05 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.13), residues: 3960 helix: 1.61 (0.12), residues: 1830 sheet: -0.56 (0.21), residues: 474 loop : 0.74 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 7 TYR 0.017 0.002 TYR F 460 PHE 0.012 0.002 PHE D 386 TRP 0.008 0.001 TRP A 498 HIS 0.005 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00355 (33072) covalent geometry : angle 0.53259 (44922) hydrogen bonds : bond 0.04148 ( 1620) hydrogen bonds : angle 5.09395 ( 4533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12399.02 seconds wall clock time: 211 minutes 48.02 seconds (12708.02 seconds total)