Starting phenix.real_space_refine on Fri Jun 27 16:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghd_40041/06_2025/8ghd_40041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghd_40041/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghd_40041/06_2025/8ghd_40041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghd_40041/06_2025/8ghd_40041.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghd_40041/06_2025/8ghd_40041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghd_40041/06_2025/8ghd_40041.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.83, per 1000 atoms: 0.52 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: 7.05 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.38 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: 11.37 Time building geometry restraints manager: 8.42 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 64.860 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.130 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.580 ------------------------------------------------------------------------------- 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 : 4.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (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 TRP 0.016 0.002 TRP C 208 HIS 0.009 0.002 HIS F 609 PHE 0.016 0.003 PHE C 228 TYR 0.018 0.003 TYR E 474 ARG 0.030 0.002 ARG F 98 Details of bonding type rmsd hydrogen bonds : bond 0.13382 ( 1620) hydrogen bonds : angle 6.89246 ( 4533) covalent geometry : bond 0.00505 (33072) covalent geometry : angle 0.84296 (44922) *********************** 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 : 3.368 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 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: 0.8152 (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: 0.7549 (tp30) REVERT: E 5 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.6927 (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 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: 1.9198 time to fit residues: 1264.2626 Evaluate side-chains 433 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 310 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 359 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 596 HIS B 625 ASN C 263 GLN C 270 ASN C 596 HIS D 20 ASN D 51 HIS 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093800 restraints weight = 36617.277| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.85 r_work: 0.3145 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 33072 Z= 0.207 Angle : 0.580 8.787 44922 Z= 0.299 Chirality : 0.043 0.219 4794 Planarity : 0.006 0.085 5844 Dihedral : 6.573 59.825 4494 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.14 % Allowed : 7.71 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 3960 helix: 1.24 (0.12), residues: 1830 sheet: -0.31 (0.22), residues: 444 loop : 0.44 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 498 HIS 0.004 0.001 HIS C 127 PHE 0.020 0.002 PHE F 386 TYR 0.019 0.002 TYR B 97 ARG 0.006 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 1620) hydrogen bonds : angle 5.57657 ( 4533) covalent geometry : bond 0.00463 (33072) covalent geometry : angle 0.57955 (44922) *********************** 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 496 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 457 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7863 (tpp-160) cc_final: 0.7357 (tmm-80) REVERT: A 21 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7254 (mtt-85) REVERT: A 156 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7126 (mmt-90) REVERT: A 164 MET cc_start: 0.9149 (mmp) cc_final: 0.8833 (mmt) REVERT: A 611 LYS cc_start: 0.8829 (mmpt) cc_final: 0.8520 (mmtp) REVERT: A 653 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8318 (mtmp) REVERT: B 3 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7490 (tmm-80) REVERT: B 20 ASN cc_start: 0.8497 (m110) cc_final: 0.8164 (m-40) REVERT: B 21 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7417 (mtt-85) REVERT: B 34 GLU cc_start: 0.8460 (tt0) cc_final: 0.8101 (tm-30) REVERT: B 35 LEU cc_start: 0.8332 (mp) cc_final: 0.8115 (mp) REVERT: B 51 HIS cc_start: 0.7347 (t-90) cc_final: 0.7117 (t-90) REVERT: B 156 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7379 (mmt-90) REVERT: B 239 MET cc_start: 0.9175 (mmm) cc_final: 0.8790 (mmm) REVERT: B 257 MET cc_start: 0.8836 (mmt) cc_final: 0.8494 (mmt) REVERT: B 259 GLU cc_start: 0.8315 (tt0) cc_final: 0.7831 (pm20) REVERT: B 568 THR cc_start: 0.9133 (p) cc_final: 0.8886 (p) REVERT: B 591 MET cc_start: 0.9180 (mtp) cc_final: 0.8933 (mtp) REVERT: C 3 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7501 (tmm-80) REVERT: C 20 ASN cc_start: 0.8428 (m110) cc_final: 0.8127 (m-40) REVERT: C 21 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7416 (mtt-85) REVERT: C 34 GLU cc_start: 0.8455 (tt0) cc_final: 0.8083 (tm-30) REVERT: C 51 HIS cc_start: 0.7316 (t-90) cc_final: 0.7091 (t-90) REVERT: C 156 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7389 (mmt-90) REVERT: C 175 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7937 (mm-30) REVERT: C 239 MET cc_start: 0.9201 (mmm) cc_final: 0.8762 (mmm) REVERT: C 591 MET cc_start: 0.9156 (mtp) cc_final: 0.8853 (mtp) REVERT: C 633 LYS cc_start: 0.8760 (tttt) cc_final: 0.8530 (tttm) REVERT: D 3 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7430 (tmm-80) REVERT: D 21 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7338 (mtt-85) REVERT: D 34 GLU cc_start: 0.8501 (tt0) cc_final: 0.8114 (tm-30) REVERT: D 45 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7505 (mt-10) REVERT: D 156 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7119 (mmp80) REVERT: D 164 MET cc_start: 0.9067 (mmp) cc_final: 0.8772 (mmt) REVERT: D 239 MET cc_start: 0.9194 (mmm) cc_final: 0.8961 (mmm) REVERT: D 571 ASP cc_start: 0.7957 (m-30) cc_final: 0.7687 (m-30) REVERT: D 632 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7689 (tp30) REVERT: D 650 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: D 653 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8098 (mtmp) REVERT: E 3 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7571 (tmm-80) REVERT: E 5 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7848 (ttp-170) REVERT: E 21 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7481 (mtt-85) REVERT: E 48 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7533 (tt0) REVERT: E 68 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7119 (t70) REVERT: E 138 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8543 (pt) REVERT: E 156 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7163 (mmt-90) REVERT: E 159 ASP cc_start: 0.8715 (m-30) cc_final: 0.8398 (m-30) REVERT: E 239 MET cc_start: 0.9133 (mmm) cc_final: 0.8748 (mmm) REVERT: E 259 GLU cc_start: 0.8400 (tt0) cc_final: 0.7845 (pm20) REVERT: E 270 ASN cc_start: 0.8864 (t0) cc_final: 0.8653 (t0) REVERT: E 650 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: F 3 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7415 (tmm-80) REVERT: F 5 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7366 (tpp80) REVERT: F 20 ASN cc_start: 0.8364 (m110) cc_final: 0.7941 (m-40) REVERT: F 21 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7700 (mtt-85) REVERT: F 48 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7354 (tp30) REVERT: F 156 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7101 (mmt-90) REVERT: F 159 ASP cc_start: 0.8716 (m-30) cc_final: 0.8410 (m-30) REVERT: F 611 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8401 (mmtm) REVERT: F 650 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: F 653 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8129 (mtmp) outliers start: 39 outliers final: 12 residues processed: 482 average time/residue: 2.0358 time to fit residues: 1135.0173 Evaluate side-chains 441 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 421 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 E residue 650 GLU Chi-restraints excluded: chain F residue 568 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 272 optimal weight: 0.7980 chunk 393 optimal weight: 0.9980 chunk 343 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 291 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 400 ASN B 263 GLN B 270 ASN B 625 ASN C 263 GLN C 270 ASN D 263 GLN D 625 ASN E 38 GLN E 263 GLN F 51 HIS 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 = 0.3614 r_free = 0.3614 target = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095445 restraints weight = 36112.251| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.86 r_work: 0.3171 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33072 Z= 0.138 Angle : 0.520 7.358 44922 Z= 0.268 Chirality : 0.041 0.245 4794 Planarity : 0.005 0.077 5844 Dihedral : 6.350 59.795 4494 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.61 % Allowed : 8.70 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 3960 helix: 1.48 (0.12), residues: 1824 sheet: -0.40 (0.22), residues: 444 loop : 0.52 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 208 HIS 0.005 0.001 HIS F 51 PHE 0.012 0.001 PHE D 386 TYR 0.017 0.002 TYR F 460 ARG 0.006 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1620) hydrogen bonds : angle 5.34010 ( 4533) covalent geometry : bond 0.00304 (33072) covalent geometry : angle 0.52022 (44922) *********************** 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 497 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 442 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7344 (tmm-80) REVERT: A 21 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7237 (mtt-85) REVERT: A 156 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7214 (mmt-90) REVERT: A 611 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8562 (mmtp) REVERT: A 650 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: A 653 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8211 (mtmp) REVERT: B 3 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7434 (tmm-80) REVERT: B 21 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7336 (mtt-85) REVERT: B 156 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7366 (mmt-90) REVERT: B 239 MET cc_start: 0.9141 (mmm) cc_final: 0.8892 (mmm) REVERT: B 266 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8362 (ttpp) REVERT: B 591 MET cc_start: 0.9184 (mtp) cc_final: 0.8974 (mtp) REVERT: C 3 ARG cc_start: 0.7733 (tpp-160) cc_final: 0.7404 (tmm-80) REVERT: C 20 ASN cc_start: 0.8502 (m110) cc_final: 0.8199 (m-40) REVERT: C 21 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7309 (mtt-85) REVERT: C 51 HIS cc_start: 0.7265 (t-90) cc_final: 0.7059 (t-90) REVERT: C 156 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7385 (mmt-90) REVERT: C 175 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7932 (mm-30) REVERT: C 239 MET cc_start: 0.9157 (mmm) cc_final: 0.8806 (mmm) REVERT: C 591 MET cc_start: 0.9163 (mtp) cc_final: 0.8928 (mtp) REVERT: C 633 LYS cc_start: 0.8729 (tttt) cc_final: 0.8495 (tttm) REVERT: D 3 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7362 (tmm-80) REVERT: D 21 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7347 (mtt-85) REVERT: D 45 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 131 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: D 156 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7202 (mmp80) REVERT: D 164 MET cc_start: 0.9068 (mmp) cc_final: 0.8798 (mmt) REVERT: D 476 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: D 571 ASP cc_start: 0.7950 (m-30) cc_final: 0.7662 (m-30) REVERT: D 632 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7729 (tp30) REVERT: D 650 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: D 653 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8077 (mtmp) REVERT: E 3 ARG cc_start: 0.7842 (tpp-160) cc_final: 0.7593 (tmm160) REVERT: E 21 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7434 (mtt-85) REVERT: E 48 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7686 (mt-10) REVERT: E 68 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7050 (t70) REVERT: E 156 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7156 (mmt-90) REVERT: E 159 ASP cc_start: 0.8723 (m-30) cc_final: 0.8414 (m-30) REVERT: E 239 MET cc_start: 0.9105 (mmm) cc_final: 0.8738 (mmm) REVERT: E 259 GLU cc_start: 0.8424 (tt0) cc_final: 0.7844 (pm20) REVERT: E 270 ASN cc_start: 0.8864 (t0) cc_final: 0.8624 (t0) REVERT: E 650 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: F 3 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7423 (tmm-80) REVERT: F 20 ASN cc_start: 0.8458 (m110) cc_final: 0.8079 (m-40) REVERT: F 21 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7569 (mtt-85) REVERT: F 155 ASP cc_start: 0.8542 (m-30) cc_final: 0.8306 (m-30) REVERT: F 156 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7066 (mmt-90) REVERT: F 159 ASP cc_start: 0.8722 (m-30) cc_final: 0.8402 (m-30) REVERT: F 168 GLU cc_start: 0.7319 (mp0) cc_final: 0.7054 (mp0) REVERT: F 611 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8416 (mmtm) REVERT: F 650 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: F 653 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8128 (mtmp) outliers start: 55 outliers final: 20 residues processed: 479 average time/residue: 1.7953 time to fit residues: 989.0048 Evaluate side-chains 452 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 422 time to evaluate : 3.567 ------------------------------------------------------------------------------- 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 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 C residue 650 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 138 ILE 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 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 138 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 224 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 356 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 296 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 B 20 ASN B 84 GLN B 263 GLN B 270 ASN C 263 GLN C 270 ASN D 84 GLN D 263 GLN E 38 GLN E 263 GLN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN F 270 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091428 restraints weight = 36145.870| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.86 r_work: 0.3102 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33072 Z= 0.234 Angle : 0.586 10.362 44922 Z= 0.299 Chirality : 0.044 0.243 4794 Planarity : 0.005 0.094 5844 Dihedral : 6.583 58.131 4494 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.55 % Allowed : 9.57 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.13), residues: 3960 helix: 1.44 (0.12), residues: 1806 sheet: -0.65 (0.21), residues: 474 loop : 0.68 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 208 HIS 0.006 0.001 HIS E 540 PHE 0.017 0.002 PHE F 386 TYR 0.020 0.002 TYR E 460 ARG 0.005 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1620) hydrogen bonds : angle 5.40761 ( 4533) covalent geometry : bond 0.00530 (33072) covalent geometry : angle 0.58626 (44922) *********************** 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 493 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 440 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7377 (tmm-80) REVERT: A 21 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7262 (mtt-85) REVERT: A 119 ASN cc_start: 0.8947 (t0) cc_final: 0.8705 (t0) REVERT: A 156 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7265 (mmp80) REVERT: A 611 LYS cc_start: 0.8932 (mmpt) cc_final: 0.8574 (mmtm) REVERT: A 650 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8634 (mm-30) REVERT: A 653 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8334 (mtmp) REVERT: B 3 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7478 (tmm-80) REVERT: B 5 ARG cc_start: 0.8357 (tpp-160) cc_final: 0.7072 (tpp80) REVERT: B 21 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7458 (mtt-85) REVERT: B 156 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7392 (mmt-90) REVERT: B 259 GLU cc_start: 0.8310 (tt0) cc_final: 0.7847 (pm20) REVERT: B 591 MET cc_start: 0.9178 (mtp) cc_final: 0.8973 (mtp) REVERT: B 636 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8496 (mttt) REVERT: B 653 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8406 (mtmm) REVERT: C 3 ARG cc_start: 0.7762 (tpp-160) cc_final: 0.7388 (tmm-80) REVERT: C 21 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7354 (mtt-85) REVERT: C 51 HIS cc_start: 0.7341 (t-90) cc_final: 0.7123 (t-90) REVERT: C 138 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8608 (pt) REVERT: C 156 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7338 (mmp80) REVERT: C 175 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7964 (mm-30) REVERT: C 239 MET cc_start: 0.9257 (mmm) cc_final: 0.8961 (mmm) REVERT: C 591 MET cc_start: 0.9175 (mtp) cc_final: 0.8844 (mtp) REVERT: C 653 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8437 (mtmm) REVERT: D 3 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7372 (tmm-80) REVERT: D 21 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7385 (mtt-85) REVERT: D 131 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: D 156 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7211 (mmp80) REVERT: D 632 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7763 (tp30) REVERT: D 650 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: E 3 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7595 (tmm160) REVERT: E 21 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7322 (mtt-85) REVERT: E 48 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7691 (tt0) REVERT: E 66 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8226 (ttm-80) REVERT: E 156 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7238 (mmt-90) REVERT: E 159 ASP cc_start: 0.8765 (m-30) cc_final: 0.8447 (m-30) REVERT: E 239 MET cc_start: 0.9260 (mmm) cc_final: 0.8994 (mmm) REVERT: E 259 GLU cc_start: 0.8418 (tt0) cc_final: 0.7829 (pm20) REVERT: E 270 ASN cc_start: 0.8895 (t0) cc_final: 0.8606 (t0) REVERT: F 21 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7683 (mtt-85) REVERT: F 156 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7138 (mmt-90) REVERT: F 159 ASP cc_start: 0.8771 (m-30) cc_final: 0.8523 (m-30) REVERT: F 568 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8774 (p) REVERT: F 650 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: F 653 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8155 (mtmp) outliers start: 53 outliers final: 23 residues processed: 469 average time/residue: 1.8491 time to fit residues: 995.2720 Evaluate side-chains 441 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 407 time to evaluate : 3.479 ------------------------------------------------------------------------------- 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 301 VAL Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 476 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 653 LYS 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 35 LEU 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 568 THR 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 89 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 349 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 B 263 GLN B 270 ASN C 263 GLN C 270 ASN D 38 GLN D 84 GLN D 198 ASN D 263 GLN D 625 ASN E 198 ASN E 263 GLN F 68 HIS F 198 ASN F 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094140 restraints weight = 35283.402| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.83 r_work: 0.3146 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33072 Z= 0.157 Angle : 0.528 8.905 44922 Z= 0.271 Chirality : 0.041 0.221 4794 Planarity : 0.005 0.104 5844 Dihedral : 6.321 56.472 4494 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.61 % Allowed : 10.74 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 3960 helix: 1.46 (0.12), residues: 1830 sheet: -0.75 (0.21), residues: 474 loop : 0.70 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.006 0.001 HIS D 540 PHE 0.012 0.002 PHE B 482 TYR 0.017 0.002 TYR F 460 ARG 0.006 0.000 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1620) hydrogen bonds : angle 5.26655 ( 4533) covalent geometry : bond 0.00353 (33072) covalent geometry : angle 0.52782 (44922) *********************** 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 479 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 424 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7448 (tmm-80) REVERT: A 21 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7209 (mtt-85) REVERT: A 156 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7279 (mmp80) REVERT: A 611 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8577 (mmtp) REVERT: A 653 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8272 (mtmp) REVERT: B 3 ARG cc_start: 0.7822 (tpp-160) cc_final: 0.7529 (tmm-80) REVERT: B 5 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7573 (tpp80) REVERT: B 21 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7426 (mtt-85) REVERT: B 156 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7384 (mmt-90) REVERT: B 653 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8338 (mtmm) REVERT: C 3 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7377 (tmm-80) REVERT: C 21 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7324 (mtt-85) REVERT: C 45 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7368 (mt-10) REVERT: C 51 HIS cc_start: 0.7093 (t-90) cc_final: 0.6854 (t-90) REVERT: C 138 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8572 (pt) REVERT: C 156 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7277 (mmp80) REVERT: C 175 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7982 (mm-30) REVERT: C 239 MET cc_start: 0.9201 (mmm) cc_final: 0.8973 (mmm) REVERT: C 635 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: C 653 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8391 (mtmm) REVERT: D 3 ARG cc_start: 0.7830 (tpp-160) cc_final: 0.7403 (tmm-80) REVERT: D 21 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7445 (mtt-85) REVERT: D 131 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: D 156 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7198 (mmp80) REVERT: D 632 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7770 (tp30) REVERT: D 650 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8013 (mm-30) REVERT: D 653 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8009 (mtmp) REVERT: E 3 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7607 (tmm160) REVERT: E 7 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8483 (mtp85) REVERT: E 21 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7290 (mtt-85) REVERT: E 48 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7697 (tp30) REVERT: E 66 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8198 (ttm-80) REVERT: E 156 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7236 (mmt-90) REVERT: E 159 ASP cc_start: 0.8739 (m-30) cc_final: 0.8443 (m-30) REVERT: E 239 MET cc_start: 0.9154 (mmm) cc_final: 0.8929 (mmm) REVERT: E 270 ASN cc_start: 0.8900 (t0) cc_final: 0.8626 (t0) REVERT: F 3 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.7240 (tmm-80) REVERT: F 48 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7565 (mm-30) REVERT: F 156 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7106 (mmt-90) REVERT: F 159 ASP cc_start: 0.8763 (m-30) cc_final: 0.8492 (m-30) REVERT: F 636 LYS cc_start: 0.8733 (mttt) cc_final: 0.8519 (mptt) REVERT: F 650 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: F 653 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8122 (mtmp) outliers start: 55 outliers final: 27 residues processed: 459 average time/residue: 1.8250 time to fit residues: 964.1103 Evaluate side-chains 448 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 410 time to evaluate : 3.364 ------------------------------------------------------------------------------- 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 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 635 GLU Chi-restraints excluded: chain C residue 636 LYS 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 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 66 ARG 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 F residue 35 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 124 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 376 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 B 84 GLN B 270 ASN C 84 GLN C 270 ASN D 38 GLN D 84 GLN D 198 ASN D 263 GLN E 198 ASN F 68 HIS F 198 ASN F 270 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093526 restraints weight = 35423.077| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.83 r_work: 0.3137 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33072 Z= 0.178 Angle : 0.540 7.995 44922 Z= 0.276 Chirality : 0.041 0.210 4794 Planarity : 0.005 0.104 5844 Dihedral : 6.337 56.078 4494 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.63 % Allowed : 11.21 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 3960 helix: 1.48 (0.12), residues: 1830 sheet: -0.73 (0.21), residues: 474 loop : 0.70 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.006 0.001 HIS D 540 PHE 0.012 0.002 PHE D 386 TYR 0.017 0.002 TYR E 460 ARG 0.007 0.000 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 1620) hydrogen bonds : angle 5.24939 ( 4533) covalent geometry : bond 0.00402 (33072) covalent geometry : angle 0.53996 (44922) *********************** 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 471 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 415 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7432 (tmm-80) REVERT: A 21 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7207 (mtt-85) REVERT: A 156 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7278 (mmp80) REVERT: A 611 LYS cc_start: 0.8908 (mmpt) cc_final: 0.8549 (mmtm) REVERT: A 653 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8310 (mtmp) REVERT: B 3 ARG cc_start: 0.7777 (tpp-160) cc_final: 0.7524 (tmm-80) REVERT: B 5 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7630 (tpp80) REVERT: B 21 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7434 (mtt-85) REVERT: B 156 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7365 (mmt-90) REVERT: B 259 GLU cc_start: 0.8278 (tt0) cc_final: 0.7843 (pm20) REVERT: B 653 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8351 (mtmm) REVERT: C 3 ARG cc_start: 0.7673 (tpp-160) cc_final: 0.7368 (tmm-80) REVERT: C 21 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7314 (mtt-85) REVERT: C 45 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 138 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (pt) REVERT: C 156 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7284 (mmp80) REVERT: C 175 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7992 (mm-30) REVERT: C 239 MET cc_start: 0.9225 (mmm) cc_final: 0.8988 (mmm) REVERT: C 568 THR cc_start: 0.9134 (p) cc_final: 0.8848 (p) REVERT: C 635 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: C 653 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: D 3 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7358 (tmm-80) REVERT: D 5 ARG cc_start: 0.8291 (ttt90) cc_final: 0.7050 (tpp80) REVERT: D 21 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7433 (mtt-85) REVERT: D 131 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: D 156 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7196 (mmp80) REVERT: D 308 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8483 (p0) REVERT: D 632 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7770 (tp30) REVERT: D 650 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: E 3 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7562 (tmm160) REVERT: E 21 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7287 (mtt-85) REVERT: E 48 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 66 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8209 (ttm-80) REVERT: E 156 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7245 (mmt-90) REVERT: E 159 ASP cc_start: 0.8741 (m-30) cc_final: 0.8445 (m-30) REVERT: E 239 MET cc_start: 0.9194 (mmm) cc_final: 0.8957 (mmm) REVERT: E 270 ASN cc_start: 0.8894 (t0) cc_final: 0.8615 (t0) REVERT: F 3 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7184 (tmm-80) REVERT: F 48 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7522 (mm-30) REVERT: F 51 HIS cc_start: 0.7155 (t70) cc_final: 0.6950 (t-90) REVERT: F 155 ASP cc_start: 0.8490 (m-30) cc_final: 0.8284 (m-30) REVERT: F 156 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7153 (mmt-90) REVERT: F 159 ASP cc_start: 0.8777 (m-30) cc_final: 0.8530 (m-30) REVERT: F 249 SER cc_start: 0.9069 (m) cc_final: 0.8712 (p) REVERT: F 568 THR cc_start: 0.9022 (p) cc_final: 0.8765 (p) REVERT: F 650 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: F 653 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8122 (mtmp) outliers start: 56 outliers final: 27 residues processed: 449 average time/residue: 1.8866 time to fit residues: 976.1825 Evaluate side-chains 445 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 407 time to evaluate : 3.794 ------------------------------------------------------------------------------- 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 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 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 183 LEU 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 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 35 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 383 optimal weight: 6.9990 chunk 259 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 254 optimal weight: 0.0970 chunk 345 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 344 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- 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 B 263 GLN B 270 ASN C 270 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 84 GLN D 198 ASN D 263 GLN E 198 ASN E 263 GLN F 68 HIS F 198 ASN F 270 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094873 restraints weight = 35129.035| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.83 r_work: 0.3158 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33072 Z= 0.147 Angle : 0.518 7.796 44922 Z= 0.266 Chirality : 0.040 0.201 4794 Planarity : 0.005 0.107 5844 Dihedral : 6.234 56.399 4494 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.13), residues: 3960 helix: 1.54 (0.12), residues: 1830 sheet: -0.72 (0.21), residues: 474 loop : 0.71 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.005 0.001 HIS D 540 PHE 0.010 0.001 PHE B 482 TYR 0.016 0.002 TYR F 460 ARG 0.009 0.000 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 1620) hydrogen bonds : angle 5.18571 ( 4533) covalent geometry : bond 0.00329 (33072) covalent geometry : angle 0.51830 (44922) *********************** 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 481 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 422 time to evaluate : 3.990 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7412 (tmm-80) REVERT: A 21 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7176 (mtt-85) REVERT: A 156 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7312 (mmt-90) REVERT: A 611 LYS cc_start: 0.8906 (mmpt) cc_final: 0.8575 (mmtp) REVERT: A 653 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8250 (mtmp) REVERT: B 3 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7528 (tmm-80) REVERT: B 5 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7878 (tpt-90) REVERT: B 21 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7433 (mtt-85) REVERT: B 156 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7386 (mmt-90) REVERT: B 259 GLU cc_start: 0.8247 (tt0) cc_final: 0.7782 (pm20) REVERT: B 653 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: C 3 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7370 (tmm-80) REVERT: C 5 ARG cc_start: 0.8239 (tpp-160) cc_final: 0.8008 (tpp80) REVERT: C 21 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7307 (mtt-85) REVERT: C 45 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 138 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (pt) REVERT: C 156 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7277 (mmp80) REVERT: C 175 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7972 (mm-30) REVERT: C 239 MET cc_start: 0.9194 (mmm) cc_final: 0.8918 (mmm) REVERT: C 568 THR cc_start: 0.9126 (p) cc_final: 0.8874 (p) REVERT: C 635 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: C 653 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8380 (mtmm) REVERT: D 3 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7382 (tmm-80) REVERT: D 21 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7434 (mtt-85) REVERT: D 131 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: D 156 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7188 (mmp80) REVERT: D 469 GLU cc_start: 0.8649 (pt0) cc_final: 0.8443 (pt0) REVERT: D 632 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7774 (tp30) REVERT: D 650 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: D 653 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8006 (mtmp) REVERT: E 3 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7537 (tmm160) REVERT: E 21 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7284 (mtt-85) REVERT: E 48 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7713 (tp30) REVERT: E 66 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8199 (ttm-80) REVERT: E 156 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7244 (mmt-90) REVERT: E 159 ASP cc_start: 0.8732 (m-30) cc_final: 0.8438 (m-30) REVERT: E 239 MET cc_start: 0.9164 (mmm) cc_final: 0.8942 (mmm) REVERT: E 270 ASN cc_start: 0.8899 (t0) cc_final: 0.8654 (t0) REVERT: F 3 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7254 (tmm-80) REVERT: F 45 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7571 (mt-10) REVERT: F 48 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7501 (mm-30) REVERT: F 51 HIS cc_start: 0.7092 (t70) cc_final: 0.6827 (t-90) REVERT: F 156 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7150 (mmt-90) REVERT: F 159 ASP cc_start: 0.8759 (m-30) cc_final: 0.8513 (m-30) REVERT: F 476 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: F 568 THR cc_start: 0.9013 (p) cc_final: 0.8751 (p) REVERT: F 650 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: F 653 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8089 (mtmp) outliers start: 59 outliers final: 22 residues processed: 458 average time/residue: 1.9934 time to fit residues: 1053.0337 Evaluate side-chains 445 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 411 time to evaluate : 3.420 ------------------------------------------------------------------------------- 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 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 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 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 35 LEU Chi-restraints excluded: chain F residue 138 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 222 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN 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 38 GLN E 198 ASN F 68 HIS 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 = 0.3593 r_free = 0.3593 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094113 restraints weight = 34942.114| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.82 r_work: 0.3146 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33072 Z= 0.168 Angle : 0.534 8.614 44922 Z= 0.273 Chirality : 0.041 0.199 4794 Planarity : 0.005 0.120 5844 Dihedral : 6.281 58.411 4494 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.40 % Allowed : 11.94 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.13), residues: 3960 helix: 1.52 (0.12), residues: 1830 sheet: -0.64 (0.21), residues: 474 loop : 0.71 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 208 HIS 0.006 0.001 HIS D 540 PHE 0.012 0.002 PHE D 386 TYR 0.017 0.002 TYR F 460 ARG 0.009 0.000 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1620) hydrogen bonds : angle 5.19267 ( 4533) covalent geometry : bond 0.00381 (33072) covalent geometry : angle 0.53424 (44922) *********************** 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 468 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 420 time to evaluate : 3.472 Fit side-chains REVERT: A 3 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7398 (tmm-80) REVERT: A 21 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7189 (mtt-85) REVERT: A 119 ASN cc_start: 0.8958 (t0) cc_final: 0.8705 (t0) REVERT: A 156 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7325 (mmt-90) REVERT: A 611 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8567 (mmtm) REVERT: A 653 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8234 (mtmp) REVERT: B 3 ARG cc_start: 0.7769 (tpp-160) cc_final: 0.7492 (tmm-80) REVERT: B 5 ARG cc_start: 0.8135 (tpp-160) cc_final: 0.7921 (tpt-90) REVERT: B 21 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7430 (mtt-85) REVERT: B 45 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 51 HIS cc_start: 0.6823 (t-90) cc_final: 0.6572 (m-70) REVERT: B 156 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7395 (mmt-90) REVERT: B 259 GLU cc_start: 0.8234 (tt0) cc_final: 0.7778 (pm20) REVERT: B 653 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8364 (mtmm) REVERT: C 3 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7433 (tmm-80) REVERT: C 5 ARG cc_start: 0.8270 (tpp-160) cc_final: 0.7402 (tpp80) REVERT: C 21 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7313 (mtt-85) REVERT: C 45 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7416 (mt-10) REVERT: C 51 HIS cc_start: 0.7153 (m-70) cc_final: 0.6815 (t-90) REVERT: C 138 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8598 (pt) REVERT: C 156 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7273 (mmp80) REVERT: C 175 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7990 (mm-30) REVERT: C 239 MET cc_start: 0.9228 (mmm) cc_final: 0.8994 (mmm) REVERT: C 568 THR cc_start: 0.9121 (p) cc_final: 0.8889 (p) REVERT: C 635 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: C 653 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8395 (mtmm) REVERT: D 3 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7391 (tmm-80) REVERT: D 21 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7446 (mtt-85) REVERT: D 51 HIS cc_start: 0.7442 (m-70) cc_final: 0.7140 (t-90) REVERT: D 131 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: D 156 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7183 (mmp80) REVERT: D 469 GLU cc_start: 0.8650 (pt0) cc_final: 0.8448 (pt0) REVERT: D 632 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7769 (tp30) REVERT: D 650 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: D 653 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.7989 (mtmp) REVERT: E 3 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7517 (tmm160) REVERT: E 21 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7295 (mtt-85) REVERT: E 48 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7772 (tp30) REVERT: E 66 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8201 (ttm-80) REVERT: E 156 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7230 (mmt-90) REVERT: E 159 ASP cc_start: 0.8736 (m-30) cc_final: 0.8441 (m-30) REVERT: E 239 MET cc_start: 0.9193 (mmm) cc_final: 0.8958 (mmm) REVERT: E 270 ASN cc_start: 0.8901 (t0) cc_final: 0.8656 (t0) REVERT: F 3 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7222 (tmm-80) REVERT: F 45 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7527 (mt-10) REVERT: F 48 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7476 (mm-30) REVERT: F 156 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7121 (mmt-90) REVERT: F 159 ASP cc_start: 0.8767 (m-30) cc_final: 0.8517 (m-30) REVERT: F 568 THR cc_start: 0.9024 (p) cc_final: 0.8767 (p) REVERT: F 650 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: F 653 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8101 (mtmp) outliers start: 48 outliers final: 25 residues processed: 449 average time/residue: 1.8178 time to fit residues: 941.0121 Evaluate side-chains 442 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 406 time to evaluate : 3.528 ------------------------------------------------------------------------------- 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 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 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 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 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 35 LEU Chi-restraints excluded: chain F residue 138 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 370 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 355 optimal weight: 0.0000 chunk 354 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 161 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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** E 198 ASN F 68 HIS F 198 ASN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096921 restraints weight = 35055.119| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.82 r_work: 0.3162 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2182 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= 0.115 Angle : 0.504 9.068 44922 Z= 0.258 Chirality : 0.040 0.202 4794 Planarity : 0.005 0.114 5844 Dihedral : 6.113 57.389 4494 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.23 % Allowed : 12.05 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.13), residues: 3960 helix: 1.64 (0.12), residues: 1824 sheet: -0.62 (0.21), residues: 474 loop : 0.73 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.004 0.001 HIS D 540 PHE 0.009 0.001 PHE A 174 TYR 0.015 0.002 TYR E 139 ARG 0.009 0.000 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 1620) hydrogen bonds : angle 5.08971 ( 4533) covalent geometry : bond 0.00255 (33072) covalent geometry : angle 0.50356 (44922) *********************** 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 474 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 432 time to evaluate : 3.723 Fit side-chains REVERT: A 3 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7416 (tmm-80) REVERT: A 21 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7146 (mtt-85) REVERT: A 156 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7318 (mmt-90) REVERT: A 611 LYS cc_start: 0.8884 (mmpt) cc_final: 0.8567 (mmtp) REVERT: A 653 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8165 (mtmp) REVERT: B 3 ARG cc_start: 0.7748 (tpp-160) cc_final: 0.7478 (tmm-80) REVERT: B 5 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7648 (tpt-90) REVERT: B 21 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7355 (mtt-85) REVERT: B 45 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 156 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7388 (mmt-90) REVERT: B 653 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8268 (mtmm) REVERT: C 3 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7448 (tmm-80) REVERT: C 5 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7629 (tpt-90) REVERT: C 21 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7276 (mtt-85) REVERT: C 45 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 51 HIS cc_start: 0.7129 (m-70) cc_final: 0.6812 (t-90) REVERT: C 156 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7282 (mmp80) REVERT: C 175 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7956 (mm-30) REVERT: C 239 MET cc_start: 0.9183 (mmm) cc_final: 0.8952 (mmm) REVERT: C 568 THR cc_start: 0.9112 (p) cc_final: 0.8889 (p) REVERT: C 635 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: C 653 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: D 3 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.7440 (tmm-80) REVERT: D 21 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7435 (mtt-85) REVERT: D 51 HIS cc_start: 0.7443 (m-70) cc_final: 0.7151 (t-90) REVERT: D 156 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7201 (mmp80) REVERT: D 476 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: D 650 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: D 653 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.7985 (mtmp) REVERT: E 3 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7458 (tmm160) REVERT: E 21 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7262 (mtt-85) REVERT: E 48 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7740 (tp30) REVERT: E 66 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (ttm-80) REVERT: E 156 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7261 (mmt-90) REVERT: E 159 ASP cc_start: 0.8724 (m-30) cc_final: 0.8442 (m-30) REVERT: E 239 MET cc_start: 0.9140 (mmm) cc_final: 0.8796 (mmm) REVERT: E 270 ASN cc_start: 0.8881 (t0) cc_final: 0.8646 (t0) REVERT: F 3 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7212 (tmm-80) REVERT: F 45 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7563 (mt-10) REVERT: F 48 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7429 (mm-30) REVERT: F 156 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7114 (mmt-90) REVERT: F 159 ASP cc_start: 0.8755 (m-30) cc_final: 0.8487 (m-30) REVERT: F 249 SER cc_start: 0.9058 (m) cc_final: 0.8746 (p) REVERT: F 568 THR cc_start: 0.9006 (p) cc_final: 0.8750 (p) REVERT: F 650 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: F 653 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8067 (mtmp) outliers start: 42 outliers final: 18 residues processed: 459 average time/residue: 1.7803 time to fit residues: 945.4496 Evaluate side-chains 447 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 419 time to evaluate : 3.519 ------------------------------------------------------------------------------- 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 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 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 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 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 319 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 268 optimal weight: 0.4980 chunk 232 optimal weight: 4.9990 chunk 353 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095772 restraints weight = 34947.187| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.82 r_work: 0.3174 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33072 Z= 0.141 Angle : 0.519 7.755 44922 Z= 0.265 Chirality : 0.040 0.199 4794 Planarity : 0.005 0.110 5844 Dihedral : 6.159 59.999 4494 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.17 % Allowed : 12.46 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.13), residues: 3960 helix: 1.65 (0.12), residues: 1824 sheet: -0.58 (0.21), residues: 474 loop : 0.74 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.005 0.001 HIS A 540 PHE 0.010 0.001 PHE D 386 TYR 0.016 0.002 TYR F 460 ARG 0.008 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1620) hydrogen bonds : angle 5.08340 ( 4533) covalent geometry : bond 0.00318 (33072) covalent geometry : angle 0.51864 (44922) ********************** 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 465 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 425 time to evaluate : 3.371 Fit side-chains REVERT: A 3 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7521 (tmm-80) REVERT: A 5 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.7959 (tpp-160) REVERT: A 21 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7207 (mtt-85) REVERT: A 119 ASN cc_start: 0.8964 (t0) cc_final: 0.8712 (t0) REVERT: A 156 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7331 (mmt-90) REVERT: A 611 LYS cc_start: 0.8882 (mmpt) cc_final: 0.8566 (mmtp) REVERT: A 653 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8180 (mtmp) REVERT: B 3 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7538 (tmm-80) REVERT: B 5 ARG cc_start: 0.8151 (tpp-160) cc_final: 0.7919 (tpt-90) REVERT: B 21 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7387 (mtt-85) REVERT: B 45 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 51 HIS cc_start: 0.7208 (m-70) cc_final: 0.6932 (t-90) REVERT: B 156 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7384 (mmt-90) REVERT: B 653 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: C 3 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7510 (tmm-80) REVERT: C 5 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7483 (tpt-90) REVERT: C 21 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7328 (mtt-85) REVERT: C 45 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 48 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6949 (mm-30) REVERT: C 51 HIS cc_start: 0.7241 (m-70) cc_final: 0.6955 (t-90) REVERT: C 156 ARG cc_start: 0.8006 (mtm110) cc_final: 0.7285 (mmp80) REVERT: C 175 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7987 (mm-30) REVERT: C 239 MET cc_start: 0.9215 (mmm) cc_final: 0.8942 (mmm) REVERT: C 270 ASN cc_start: 0.8894 (t0) cc_final: 0.8572 (t0) REVERT: C 568 THR cc_start: 0.9113 (p) cc_final: 0.8883 (p) REVERT: C 635 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: C 653 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: D 3 ARG cc_start: 0.7830 (tpp-160) cc_final: 0.7547 (tmm-80) REVERT: D 5 ARG cc_start: 0.8117 (tpp-160) cc_final: 0.7461 (tpp80) REVERT: D 21 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7442 (mtt-85) REVERT: D 51 HIS cc_start: 0.7522 (m-70) cc_final: 0.7320 (t-90) REVERT: D 156 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7211 (mmp80) REVERT: D 650 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: D 653 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7980 (mtmp) REVERT: E 3 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7451 (tmm160) REVERT: E 21 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7297 (mtt-85) REVERT: E 66 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8178 (ttm-80) REVERT: E 156 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7266 (mmt-90) REVERT: E 159 ASP cc_start: 0.8725 (m-30) cc_final: 0.8433 (m-30) REVERT: E 239 MET cc_start: 0.9176 (mmm) cc_final: 0.8814 (mmm) REVERT: E 270 ASN cc_start: 0.8882 (t0) cc_final: 0.8644 (t0) REVERT: E 650 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: F 3 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7251 (tmm-80) REVERT: F 45 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7529 (mt-10) REVERT: F 48 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7450 (mm-30) REVERT: F 156 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7111 (mmt-90) REVERT: F 159 ASP cc_start: 0.8761 (m-30) cc_final: 0.8496 (m-30) REVERT: F 249 SER cc_start: 0.9059 (m) cc_final: 0.8745 (p) REVERT: F 568 THR cc_start: 0.9018 (p) cc_final: 0.8759 (p) REVERT: F 632 GLU cc_start: 0.8339 (tp30) cc_final: 0.8037 (tp30) REVERT: F 650 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: F 653 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8078 (mtmp) outliers start: 40 outliers final: 18 residues processed: 451 average time/residue: 1.8194 time to fit residues: 948.4351 Evaluate side-chains 441 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 413 time to evaluate : 3.674 ------------------------------------------------------------------------------- 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 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 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 E residue 650 GLU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 439 CYS 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 389 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 361 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 299 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 84 GLN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 198 ASN F 198 ASN F 270 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096701 restraints weight = 34901.370| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.82 r_work: 0.3190 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2227 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 : 0.510 7.717 44922 Z= 0.261 Chirality : 0.040 0.202 4794 Planarity : 0.005 0.109 5844 Dihedral : 6.052 58.271 4494 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.99 % Allowed : 12.76 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 3960 helix: 1.69 (0.12), residues: 1830 sheet: -0.58 (0.21), residues: 474 loop : 0.77 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.005 0.001 HIS D 540 PHE 0.009 0.001 PHE A 174 TYR 0.021 0.002 TYR A 139 ARG 0.009 0.000 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 1620) hydrogen bonds : angle 5.05056 ( 4533) covalent geometry : bond 0.00281 (33072) covalent geometry : angle 0.50973 (44922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30417.27 seconds wall clock time: 522 minutes 56.01 seconds (31376.01 seconds total)