Starting phenix.real_space_refine on Fri Mar 22 21:11:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/03_2024/5ftm_3298_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/03_2024/5ftm_3298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/03_2024/5ftm_3298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/03_2024/5ftm_3298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/03_2024/5ftm_3298_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/03_2024/5ftm_3298_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 186 5.16 5 C 21636 2.51 5 N 6090 2.21 5 O 6606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34554 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.66, per 1000 atoms: 0.51 Number of scatterers: 34554 At special positions: 0 Unit cell: (164.268, 175.084, 102.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 186 16.00 P 30 15.00 Mg 6 11.99 O 6606 8.00 N 6090 7.00 C 21636 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 - 3.50 Amino acid : False - 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: 13.03 Conformation dependent library (CDL) restraints added in 6.0 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 30 sheets defined 37.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.77 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.210A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.520A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.732A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 430 No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 760 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.211A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.521A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 318 through 332 removed outlier: 3.733A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.517A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 402 No H-bonds generated for 'chain 'B' and resid 399 through 402' Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 604 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.594A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.565A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 760 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.211A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.521A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.596A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 318 through 332 removed outlier: 3.500A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 402 No H-bonds generated for 'chain 'C' and resid 399 through 402' Processing helix chain 'C' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 No H-bonds generated for 'chain 'C' and resid 427 through 430' Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 599 through 608 removed outlier: 3.669A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 604 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.509A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 760 Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 91 removed outlier: 4.210A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.520A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 318 through 332 removed outlier: 3.732A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 402 No H-bonds generated for 'chain 'D' and resid 399 through 402' Processing helix chain 'D' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 430 No H-bonds generated for 'chain 'D' and resid 427 through 430' Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 524 through 535 removed outlier: 4.029A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 604 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 657 " --> pdb=" O ARG D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.596A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 760 Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.210A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.520A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA E 289 " --> pdb=" O ASN E 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 318 through 332 removed outlier: 3.733A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 402 No H-bonds generated for 'chain 'E' and resid 399 through 402' Processing helix chain 'E' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 No H-bonds generated for 'chain 'E' and resid 427 through 430' Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 455 Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 567 Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 604 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 760 Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 91 removed outlier: 4.211A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.521A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 318 through 332 removed outlier: 3.732A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.517A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 No H-bonds generated for 'chain 'F' and resid 399 through 402' Processing helix chain 'F' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 No H-bonds generated for 'chain 'F' and resid 427 through 430' Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 455 Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 567 Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE F 604 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 657 " --> pdb=" O ARG F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 760 Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 56 through 59 Processing sheet with id= C, first strand: chain 'A' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 241 through 243 removed outlier: 6.180A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY A 518 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 640 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 515 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU A 642 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR A 517 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 644 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= G, first strand: chain 'B' and resid 56 through 59 Processing sheet with id= H, first strand: chain 'B' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 241 through 243 removed outlier: 6.179A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 640 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 515 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 642 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR B 517 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR B 644 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= L, first strand: chain 'C' and resid 56 through 59 Processing sheet with id= M, first strand: chain 'C' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 241 through 243 removed outlier: 6.180A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 640 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU C 515 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 642 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR C 517 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR C 644 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 39 through 41 Processing sheet with id= Q, first strand: chain 'D' and resid 56 through 59 Processing sheet with id= R, first strand: chain 'D' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 241 through 243 removed outlier: 6.179A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= V, first strand: chain 'E' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'E' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 241 through 243 removed outlier: 6.179A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 640 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 515 " --> pdb=" O ASP E 640 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU E 642 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR E 517 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR E 644 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= AA, first strand: chain 'F' and resid 56 through 59 Processing sheet with id= AB, first strand: chain 'F' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 241 through 243 removed outlier: 6.180A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 640 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2661 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: 10.94 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 13464 1.38 - 1.55: 21318 1.55 - 1.73: 54 1.73 - 1.90: 288 1.90 - 2.07: 6 Bond restraints: 35130 Sorted by residual: bond pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS A 901 " pdb=" C5 AGS A 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS E 901 " pdb=" C5 AGS E 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS B 901 " pdb=" C5 AGS B 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS C 901 " pdb=" C5 AGS C 901 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.80e+01 ... (remaining 35125 not shown) Histogram of bond angle deviations from ideal: 93.49 - 102.48: 256 102.48 - 111.46: 15324 111.46 - 120.45: 19273 120.45 - 129.44: 12463 129.44 - 138.42: 198 Bond angle restraints: 47514 Sorted by residual: angle pdb=" N GLU C 314 " pdb=" CA GLU C 314 " pdb=" C GLU C 314 " ideal model delta sigma weight residual 113.17 98.21 14.96 1.26e+00 6.30e-01 1.41e+02 angle pdb=" N GLU F 314 " pdb=" CA GLU F 314 " pdb=" C GLU F 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU D 314 " pdb=" CA GLU D 314 " pdb=" C GLU D 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU A 314 " pdb=" CA GLU A 314 " pdb=" C GLU A 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU E 314 " pdb=" CA GLU E 314 " pdb=" C GLU E 314 " ideal model delta sigma weight residual 113.17 98.25 14.92 1.26e+00 6.30e-01 1.40e+02 ... (remaining 47509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 21424 30.45 - 60.90: 296 60.90 - 91.35: 54 91.35 - 121.80: 0 121.80 - 152.24: 6 Dihedral angle restraints: 21780 sinusoidal: 9210 harmonic: 12570 Sorted by residual: dihedral pdb=" CD ARG D 377 " pdb=" NE ARG D 377 " pdb=" CZ ARG D 377 " pdb=" NH1 ARG D 377 " ideal model delta sinusoidal sigma weight residual 0.00 58.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CD ARG C 377 " pdb=" NE ARG C 377 " pdb=" CZ ARG C 377 " pdb=" NH1 ARG C 377 " ideal model delta sinusoidal sigma weight residual 0.00 58.00 -58.00 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CD ARG E 377 " pdb=" NE ARG E 377 " pdb=" CZ ARG E 377 " pdb=" NH1 ARG E 377 " ideal model delta sinusoidal sigma weight residual 0.00 57.97 -57.97 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 21777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3720 0.067 - 0.133: 1383 0.133 - 0.200: 205 0.200 - 0.266: 43 0.266 - 0.333: 1 Chirality restraints: 5352 Sorted by residual: chirality pdb=" CA ILE A 731 " pdb=" N ILE A 731 " pdb=" C ILE A 731 " pdb=" CB ILE A 731 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ARG E 313 " pdb=" N ARG E 313 " pdb=" C ARG E 313 " pdb=" CB ARG E 313 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLU C 314 " pdb=" N GLU C 314 " pdb=" C GLU C 314 " pdb=" CB GLU C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 5349 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 377 " 0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG E 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG E 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 377 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 377 " 0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG D 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 377 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 377 " 0.922 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG C 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG C 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 377 " 0.022 2.00e-02 2.50e+03 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3212 2.71 - 3.26: 36912 3.26 - 3.81: 54051 3.81 - 4.35: 69551 4.35 - 4.90: 113304 Nonbonded interactions: 277030 Sorted by model distance: nonbonded pdb=" OD1 ASP B 373 " pdb=" N ALA B 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP A 373 " pdb=" N ALA A 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP D 373 " pdb=" N ALA D 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP C 373 " pdb=" N ALA C 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP E 373 " pdb=" N ALA E 374 " model vdw 2.163 2.520 ... (remaining 277025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.030 Extract box with map and model: 6.700 Check model and map are aligned: 0.540 Set scattering table: 0.290 Process input model: 85.550 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.124 35130 Z= 0.902 Angle : 1.339 15.400 47514 Z= 0.762 Chirality : 0.067 0.333 5352 Planarity : 0.017 0.414 6234 Dihedral : 12.081 152.244 13632 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.57 % Favored : 91.71 % Rotamer: Outliers : 0.51 % Allowed : 2.53 % Favored : 96.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.69 % 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: -4.68 (0.10), residues: 4344 helix: -4.15 (0.07), residues: 1584 sheet: -2.40 (0.17), residues: 684 loop : -2.35 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP F 551 HIS 0.014 0.005 HIS C 317 PHE 0.052 0.006 PHE C 516 TYR 0.039 0.004 TYR C 138 ARG 0.016 0.002 ARG F 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 851 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5665 (t) cc_final: 0.5244 (m) REVERT: A 148 LYS cc_start: 0.6461 (mttt) cc_final: 0.6179 (mmtt) REVERT: A 173 TYR cc_start: 0.4843 (p90) cc_final: 0.4269 (p90) REVERT: A 546 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 39 VAL cc_start: 0.5699 (t) cc_final: 0.5259 (m) REVERT: B 148 LYS cc_start: 0.6494 (mttt) cc_final: 0.6268 (mmtt) REVERT: B 442 MET cc_start: 0.7469 (mmt) cc_final: 0.7126 (mmt) REVERT: B 546 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8387 (tm-30) REVERT: C 39 VAL cc_start: 0.5605 (t) cc_final: 0.5188 (m) REVERT: C 148 LYS cc_start: 0.6550 (mttt) cc_final: 0.6310 (mmtm) REVERT: C 173 TYR cc_start: 0.5009 (p90) cc_final: 0.4355 (p90) REVERT: C 393 ASP cc_start: 0.6423 (p0) cc_final: 0.6091 (p0) REVERT: C 442 MET cc_start: 0.7517 (mmt) cc_final: 0.7115 (mmt) REVERT: C 449 MET cc_start: 0.7982 (tpp) cc_final: 0.7781 (tpp) REVERT: C 478 ASP cc_start: 0.8550 (t0) cc_final: 0.8347 (m-30) REVERT: C 546 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 39 VAL cc_start: 0.5541 (t) cc_final: 0.5110 (m) REVERT: D 148 LYS cc_start: 0.6439 (mttt) cc_final: 0.6156 (mmtt) REVERT: D 173 TYR cc_start: 0.4799 (p90) cc_final: 0.4247 (p90) REVERT: D 546 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8362 (tm-30) REVERT: E 39 VAL cc_start: 0.5660 (t) cc_final: 0.5065 (m) REVERT: E 148 LYS cc_start: 0.6437 (mttt) cc_final: 0.6218 (mmtt) REVERT: E 442 MET cc_start: 0.7471 (mmt) cc_final: 0.7177 (mmt) REVERT: E 546 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8393 (tm-30) REVERT: F 39 VAL cc_start: 0.5500 (t) cc_final: 0.5060 (m) REVERT: F 148 LYS cc_start: 0.6522 (mttt) cc_final: 0.6313 (mmtm) REVERT: F 173 TYR cc_start: 0.4851 (p90) cc_final: 0.4210 (p90) REVERT: F 393 ASP cc_start: 0.6494 (p0) cc_final: 0.6211 (p0) REVERT: F 442 MET cc_start: 0.7526 (mmt) cc_final: 0.7166 (mmt) REVERT: F 546 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 19 outliers final: 0 residues processed: 864 average time/residue: 0.5889 time to fit residues: 747.7236 Evaluate side-chains 428 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 8.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 392 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 533 ASN A 538 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 538 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 538 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 533 ASN D 538 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 538 ASN ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 35130 Z= 0.316 Angle : 0.849 8.402 47514 Z= 0.430 Chirality : 0.051 0.167 5352 Planarity : 0.006 0.056 6234 Dihedral : 9.861 147.280 4926 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.72 % Favored : 93.00 % Rotamer: Outliers : 2.53 % Allowed : 8.89 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.05 (0.11), residues: 4344 helix: -2.37 (0.10), residues: 1674 sheet: -1.59 (0.18), residues: 666 loop : -1.71 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 551 HIS 0.008 0.002 HIS D 317 PHE 0.020 0.002 PHE A 516 TYR 0.021 0.003 TYR D 138 ARG 0.007 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 490 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5712 (t) cc_final: 0.5212 (m) REVERT: A 83 ARG cc_start: 0.5810 (mmt90) cc_final: 0.5424 (mmt90) REVERT: A 134 TYR cc_start: 0.6079 (m-80) cc_final: 0.5853 (m-10) REVERT: A 442 MET cc_start: 0.7347 (mmp) cc_final: 0.6926 (mmt) REVERT: A 449 MET cc_start: 0.7715 (tpp) cc_final: 0.6913 (ttm) REVERT: A 546 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 551 TRP cc_start: 0.5566 (t60) cc_final: 0.5241 (t60) REVERT: A 560 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7122 (mtp180) REVERT: A 692 GLN cc_start: 0.8157 (tp40) cc_final: 0.7866 (mm110) REVERT: B 39 VAL cc_start: 0.5693 (t) cc_final: 0.5174 (m) REVERT: B 83 ARG cc_start: 0.5751 (mmt90) cc_final: 0.5447 (mmt90) REVERT: B 93 ARG cc_start: 0.7679 (mmt90) cc_final: 0.7394 (mmt180) REVERT: B 134 TYR cc_start: 0.6025 (m-80) cc_final: 0.5637 (m-10) REVERT: B 440 GLU cc_start: 0.7284 (pm20) cc_final: 0.6170 (tp30) REVERT: B 449 MET cc_start: 0.7854 (tpp) cc_final: 0.6968 (ttm) REVERT: B 551 TRP cc_start: 0.5640 (t60) cc_final: 0.5120 (t60) REVERT: B 560 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7083 (mtp180) REVERT: B 599 ARG cc_start: 0.7674 (ptp90) cc_final: 0.6951 (ptt90) REVERT: C 39 VAL cc_start: 0.5956 (t) cc_final: 0.5452 (m) REVERT: C 393 ASP cc_start: 0.6422 (p0) cc_final: 0.6076 (p0) REVERT: C 546 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 560 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7201 (mtp180) REVERT: C 599 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7090 (ttp80) REVERT: D 39 VAL cc_start: 0.5765 (t) cc_final: 0.5243 (m) REVERT: D 83 ARG cc_start: 0.5813 (mmt90) cc_final: 0.5430 (mmt90) REVERT: D 134 TYR cc_start: 0.6083 (m-80) cc_final: 0.5828 (m-10) REVERT: D 442 MET cc_start: 0.7365 (mmp) cc_final: 0.6984 (mmt) REVERT: D 449 MET cc_start: 0.7723 (tpp) cc_final: 0.6906 (ttm) REVERT: D 546 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8380 (tm-30) REVERT: D 551 TRP cc_start: 0.5576 (t60) cc_final: 0.5240 (t60) REVERT: D 560 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7113 (mtp180) REVERT: D 692 GLN cc_start: 0.8146 (tp40) cc_final: 0.7841 (mm110) REVERT: E 39 VAL cc_start: 0.5664 (t) cc_final: 0.5263 (m) REVERT: E 83 ARG cc_start: 0.5775 (mmt90) cc_final: 0.5452 (mmt90) REVERT: E 134 TYR cc_start: 0.6062 (m-80) cc_final: 0.5655 (m-10) REVERT: E 449 MET cc_start: 0.7837 (tpp) cc_final: 0.6974 (ttm) REVERT: E 551 TRP cc_start: 0.5637 (t60) cc_final: 0.5153 (t60) REVERT: E 560 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7114 (mtp180) REVERT: E 599 ARG cc_start: 0.7670 (ptp90) cc_final: 0.6953 (ptt90) REVERT: F 39 VAL cc_start: 0.5898 (t) cc_final: 0.5423 (m) REVERT: F 134 TYR cc_start: 0.6026 (m-80) cc_final: 0.5776 (m-10) REVERT: F 449 MET cc_start: 0.7819 (tpp) cc_final: 0.7006 (ttm) REVERT: F 546 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8354 (tm-30) REVERT: F 558 ASN cc_start: 0.6201 (m110) cc_final: 0.5984 (m110) REVERT: F 560 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7183 (mtp180) REVERT: F 599 ARG cc_start: 0.7752 (ptp90) cc_final: 0.7092 (ttp80) outliers start: 94 outliers final: 61 residues processed: 559 average time/residue: 0.5278 time to fit residues: 448.6934 Evaluate side-chains 463 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 402 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 chunk 350 optimal weight: 30.0000 chunk 389 optimal weight: 30.0000 chunk 133 optimal weight: 3.9990 chunk 315 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35130 Z= 0.326 Angle : 0.782 8.468 47514 Z= 0.390 Chirality : 0.049 0.158 5352 Planarity : 0.006 0.087 6234 Dihedral : 9.477 148.362 4926 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.83 % Favored : 91.90 % Rotamer: Outliers : 3.69 % Allowed : 11.31 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.28 (0.12), residues: 4344 helix: -1.44 (0.12), residues: 1674 sheet: -1.33 (0.20), residues: 618 loop : -1.51 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 551 HIS 0.006 0.002 HIS C 384 PHE 0.021 0.002 PHE A 516 TYR 0.018 0.002 TYR A 138 ARG 0.006 0.001 ARG C 766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 423 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5393 (t) cc_final: 0.5042 (m) REVERT: A 83 ARG cc_start: 0.5825 (mmt90) cc_final: 0.5605 (mmt90) REVERT: A 134 TYR cc_start: 0.6052 (m-80) cc_final: 0.5757 (m-10) REVERT: A 442 MET cc_start: 0.7402 (mmp) cc_final: 0.6995 (mmt) REVERT: A 449 MET cc_start: 0.7754 (tpp) cc_final: 0.6908 (ttm) REVERT: A 546 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 551 TRP cc_start: 0.5591 (t60) cc_final: 0.5229 (t60) REVERT: A 692 GLN cc_start: 0.8257 (tp40) cc_final: 0.7916 (mm-40) REVERT: B 39 VAL cc_start: 0.5514 (t) cc_final: 0.5159 (m) REVERT: B 83 ARG cc_start: 0.5805 (mmt90) cc_final: 0.5467 (mmt90) REVERT: B 134 TYR cc_start: 0.6051 (m-80) cc_final: 0.5580 (m-10) REVERT: B 427 MET cc_start: 0.6081 (ttt) cc_final: 0.5726 (mmm) REVERT: B 449 MET cc_start: 0.7825 (tpp) cc_final: 0.6886 (ttm) REVERT: B 551 TRP cc_start: 0.5566 (t60) cc_final: 0.5097 (t60) REVERT: B 599 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7201 (ttp80) REVERT: C 39 VAL cc_start: 0.5901 (t) cc_final: 0.5601 (m) REVERT: C 427 MET cc_start: 0.6002 (ttt) cc_final: 0.5628 (mmm) REVERT: C 449 MET cc_start: 0.7797 (tpp) cc_final: 0.6986 (ttm) REVERT: C 546 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8380 (tm-30) REVERT: C 599 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7162 (ttp80) REVERT: D 39 VAL cc_start: 0.5425 (t) cc_final: 0.5055 (m) REVERT: D 83 ARG cc_start: 0.5854 (mmt90) cc_final: 0.5643 (mmt90) REVERT: D 134 TYR cc_start: 0.6068 (m-80) cc_final: 0.5764 (m-10) REVERT: D 442 MET cc_start: 0.7403 (mmp) cc_final: 0.7007 (mmt) REVERT: D 449 MET cc_start: 0.7763 (tpp) cc_final: 0.6889 (ttm) REVERT: D 546 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8425 (tm-30) REVERT: D 551 TRP cc_start: 0.5571 (t60) cc_final: 0.5189 (t60) REVERT: D 673 GLU cc_start: 0.8136 (mp0) cc_final: 0.7888 (mp0) REVERT: E 39 VAL cc_start: 0.5425 (t) cc_final: 0.5076 (m) REVERT: E 134 TYR cc_start: 0.6021 (m-80) cc_final: 0.5607 (m-10) REVERT: E 427 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5711 (mmm) REVERT: E 449 MET cc_start: 0.7841 (tpp) cc_final: 0.6915 (ttm) REVERT: E 551 TRP cc_start: 0.5569 (t60) cc_final: 0.5101 (t60) REVERT: E 599 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7211 (ttp80) REVERT: F 39 VAL cc_start: 0.5718 (t) cc_final: 0.5368 (m) REVERT: F 134 TYR cc_start: 0.6017 (m-80) cc_final: 0.5787 (m-10) REVERT: F 294 GLU cc_start: 0.7721 (tp30) cc_final: 0.7359 (tp30) REVERT: F 427 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5625 (mmm) REVERT: F 546 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8378 (tm-30) REVERT: F 599 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7170 (ttp80) outliers start: 137 outliers final: 95 residues processed: 522 average time/residue: 0.4886 time to fit residues: 403.1740 Evaluate side-chains 471 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 374 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 558 ASN Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 0.0070 chunk 394 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 692 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 35130 Z= 0.305 Angle : 0.737 7.627 47514 Z= 0.367 Chirality : 0.049 0.150 5352 Planarity : 0.005 0.045 6234 Dihedral : 9.264 148.230 4926 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 5.79 % Allowed : 12.06 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.87 (0.12), residues: 4344 helix: -0.94 (0.12), residues: 1674 sheet: -1.02 (0.19), residues: 690 loop : -1.48 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 551 HIS 0.006 0.002 HIS C 384 PHE 0.018 0.002 PHE A 576 TYR 0.017 0.002 TYR B 138 ARG 0.007 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 402 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5419 (t) cc_final: 0.5109 (m) REVERT: A 83 ARG cc_start: 0.5867 (mmt90) cc_final: 0.5577 (mmt90) REVERT: A 239 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8057 (ptt-90) REVERT: A 427 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5640 (mmm) REVERT: A 440 GLU cc_start: 0.7422 (pm20) cc_final: 0.6935 (mm-30) REVERT: A 442 MET cc_start: 0.7428 (mmp) cc_final: 0.7064 (mmt) REVERT: A 449 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6872 (ttm) REVERT: A 460 ASN cc_start: 0.5408 (OUTLIER) cc_final: 0.5204 (p0) REVERT: A 546 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 551 TRP cc_start: 0.5375 (t60) cc_final: 0.5130 (t60) REVERT: A 679 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7289 (p) REVERT: A 692 GLN cc_start: 0.8372 (tp40) cc_final: 0.8073 (mm-40) REVERT: B 39 VAL cc_start: 0.5406 (t) cc_final: 0.5080 (m) REVERT: B 83 ARG cc_start: 0.5841 (mmt90) cc_final: 0.5618 (mmt90) REVERT: B 427 MET cc_start: 0.6009 (ttt) cc_final: 0.5726 (mmm) REVERT: B 440 GLU cc_start: 0.7534 (pm20) cc_final: 0.6945 (mm-30) REVERT: B 449 MET cc_start: 0.7806 (tpp) cc_final: 0.6867 (ttm) REVERT: B 460 ASN cc_start: 0.5488 (OUTLIER) cc_final: 0.5210 (p0) REVERT: B 546 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 551 TRP cc_start: 0.5368 (t60) cc_final: 0.4993 (t60) REVERT: B 599 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7314 (ttp80) REVERT: C 39 VAL cc_start: 0.5705 (t) cc_final: 0.5407 (m) REVERT: C 83 ARG cc_start: 0.5928 (mmt90) cc_final: 0.5715 (mmt90) REVERT: C 427 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5698 (mmm) REVERT: C 546 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 599 ARG cc_start: 0.7865 (ptp90) cc_final: 0.7387 (ttp80) REVERT: D 39 VAL cc_start: 0.5343 (t) cc_final: 0.5024 (m) REVERT: D 83 ARG cc_start: 0.5903 (mmt90) cc_final: 0.5596 (mmt90) REVERT: D 239 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: D 427 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5727 (mmm) REVERT: D 440 GLU cc_start: 0.7451 (pm20) cc_final: 0.6949 (mm-30) REVERT: D 442 MET cc_start: 0.7451 (mmp) cc_final: 0.7086 (mmt) REVERT: D 449 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6838 (ttm) REVERT: D 460 ASN cc_start: 0.5401 (OUTLIER) cc_final: 0.5200 (p0) REVERT: D 546 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8390 (tm-30) REVERT: D 551 TRP cc_start: 0.5357 (t60) cc_final: 0.5149 (t60) REVERT: E 39 VAL cc_start: 0.5333 (t) cc_final: 0.5004 (m) REVERT: E 427 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5715 (mmm) REVERT: E 440 GLU cc_start: 0.7532 (pm20) cc_final: 0.6946 (mm-30) REVERT: E 449 MET cc_start: 0.7810 (tpp) cc_final: 0.6886 (ttm) REVERT: E 460 ASN cc_start: 0.5506 (OUTLIER) cc_final: 0.5229 (p0) REVERT: E 546 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8434 (tm-30) REVERT: E 551 TRP cc_start: 0.5354 (t60) cc_final: 0.5025 (t60) REVERT: E 599 ARG cc_start: 0.7798 (ptp90) cc_final: 0.7355 (ttp80) REVERT: F 39 VAL cc_start: 0.5626 (t) cc_final: 0.5341 (m) REVERT: F 427 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5636 (mmm) REVERT: F 440 GLU cc_start: 0.7415 (pm20) cc_final: 0.6820 (mm-30) REVERT: F 449 MET cc_start: 0.7696 (tpp) cc_final: 0.6824 (ttm) REVERT: F 494 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8211 (mm110) REVERT: F 546 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8383 (tm-30) REVERT: F 599 ARG cc_start: 0.7860 (ptp90) cc_final: 0.7364 (ttp80) outliers start: 215 outliers final: 122 residues processed: 584 average time/residue: 0.4707 time to fit residues: 440.1424 Evaluate side-chains 511 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 374 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 765 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 356 optimal weight: 0.1980 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 105 optimal weight: 0.2980 overall best weight: 5.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35130 Z= 0.284 Angle : 0.708 7.131 47514 Z= 0.352 Chirality : 0.048 0.149 5352 Planarity : 0.005 0.046 6234 Dihedral : 9.100 147.050 4926 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.44 % Favored : 92.24 % Rotamer: Outliers : 4.87 % Allowed : 13.54 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.78 (0.12), residues: 4344 helix: -0.87 (0.12), residues: 1710 sheet: -1.01 (0.19), residues: 708 loop : -1.40 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 551 HIS 0.005 0.001 HIS F 384 PHE 0.015 0.002 PHE C 576 TYR 0.016 0.002 TYR D 138 ARG 0.005 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 409 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5414 (t) cc_final: 0.5096 (m) REVERT: A 83 ARG cc_start: 0.5769 (mmt90) cc_final: 0.5496 (mmt90) REVERT: A 239 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (ptt-90) REVERT: A 317 HIS cc_start: 0.3168 (t70) cc_final: 0.2682 (t-90) REVERT: A 427 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5758 (mmm) REVERT: A 442 MET cc_start: 0.7457 (mmp) cc_final: 0.7066 (mmt) REVERT: A 449 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6864 (ttm) REVERT: A 546 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 551 TRP cc_start: 0.5248 (t60) cc_final: 0.5018 (t60) REVERT: A 679 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7272 (p) REVERT: A 692 GLN cc_start: 0.8367 (tp40) cc_final: 0.8097 (mm-40) REVERT: B 39 VAL cc_start: 0.5368 (t) cc_final: 0.5077 (m) REVERT: B 427 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5702 (mmm) REVERT: B 440 GLU cc_start: 0.7502 (pm20) cc_final: 0.6949 (mm-30) REVERT: B 449 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7504 (tpp) REVERT: B 460 ASN cc_start: 0.5418 (OUTLIER) cc_final: 0.5168 (p0) REVERT: B 494 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8193 (mm110) REVERT: B 550 MET cc_start: 0.6595 (tpt) cc_final: 0.6112 (ttp) REVERT: B 551 TRP cc_start: 0.5382 (t60) cc_final: 0.4971 (t60) REVERT: B 599 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7241 (ttp80) REVERT: C 39 VAL cc_start: 0.5580 (t) cc_final: 0.5317 (m) REVERT: C 122 THR cc_start: 0.6583 (m) cc_final: 0.6377 (p) REVERT: C 427 MET cc_start: 0.6077 (ttt) cc_final: 0.5780 (mmm) REVERT: C 449 MET cc_start: 0.7678 (tpp) cc_final: 0.6861 (ttm) REVERT: C 492 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8776 (mp) REVERT: C 494 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7982 (mm110) REVERT: C 546 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8361 (tm-30) REVERT: C 550 MET cc_start: 0.6515 (tpt) cc_final: 0.6226 (tpt) REVERT: C 599 ARG cc_start: 0.7787 (ptp90) cc_final: 0.7351 (ttp80) REVERT: D 39 VAL cc_start: 0.5422 (t) cc_final: 0.5109 (m) REVERT: D 122 THR cc_start: 0.6468 (m) cc_final: 0.6210 (p) REVERT: D 239 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8190 (ptt-90) REVERT: D 427 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5747 (mmm) REVERT: D 440 GLU cc_start: 0.7454 (pm20) cc_final: 0.6645 (tp30) REVERT: D 442 MET cc_start: 0.7456 (mmp) cc_final: 0.7067 (mmt) REVERT: D 449 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6844 (ttm) REVERT: D 546 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 551 TRP cc_start: 0.5284 (t60) cc_final: 0.5039 (t60) REVERT: E 39 VAL cc_start: 0.5370 (t) cc_final: 0.5067 (m) REVERT: E 83 ARG cc_start: 0.5860 (mmt90) cc_final: 0.5481 (mmm-85) REVERT: E 427 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5738 (mmm) REVERT: E 440 GLU cc_start: 0.7509 (pm20) cc_final: 0.6961 (mm-30) REVERT: E 449 MET cc_start: 0.7795 (tpp) cc_final: 0.7491 (tpp) REVERT: E 460 ASN cc_start: 0.5446 (OUTLIER) cc_final: 0.5194 (p0) REVERT: E 494 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8173 (mm110) REVERT: E 550 MET cc_start: 0.6595 (tpt) cc_final: 0.6120 (ttp) REVERT: E 551 TRP cc_start: 0.5369 (t60) cc_final: 0.4996 (t60) REVERT: E 599 ARG cc_start: 0.7773 (ptp90) cc_final: 0.7283 (ttp80) REVERT: E 661 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (pp) REVERT: F 39 VAL cc_start: 0.5418 (t) cc_final: 0.5142 (m) REVERT: F 122 THR cc_start: 0.6537 (m) cc_final: 0.6283 (p) REVERT: F 427 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5705 (mmm) REVERT: F 449 MET cc_start: 0.7751 (tpp) cc_final: 0.6808 (ttm) REVERT: F 492 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8775 (mp) REVERT: F 546 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8366 (tm-30) REVERT: F 599 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7316 (ttp80) outliers start: 181 outliers final: 135 residues processed: 539 average time/residue: 0.4724 time to fit residues: 404.7099 Evaluate side-chains 531 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 377 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 765 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 765 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN E 327 GLN ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 35130 Z= 0.298 Angle : 0.707 6.923 47514 Z= 0.350 Chirality : 0.048 0.147 5352 Planarity : 0.005 0.046 6234 Dihedral : 9.075 148.149 4926 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.67 % Favored : 92.06 % Rotamer: Outliers : 5.63 % Allowed : 13.68 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.79 (0.12), residues: 4344 helix: -0.91 (0.12), residues: 1746 sheet: -1.00 (0.19), residues: 708 loop : -1.39 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 551 HIS 0.005 0.001 HIS F 384 PHE 0.016 0.002 PHE A 576 TYR 0.015 0.002 TYR D 138 ARG 0.007 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 399 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5518 (t) cc_final: 0.5206 (m) REVERT: A 83 ARG cc_start: 0.5746 (mmt90) cc_final: 0.5528 (mmt90) REVERT: A 122 THR cc_start: 0.6480 (m) cc_final: 0.6227 (p) REVERT: A 158 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7002 (mmm) REVERT: A 427 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5839 (mmm) REVERT: A 442 MET cc_start: 0.7433 (mmp) cc_final: 0.7056 (mmt) REVERT: A 449 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6892 (ttm) REVERT: A 546 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 673 GLU cc_start: 0.8265 (mp0) cc_final: 0.7925 (mp0) REVERT: A 679 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7289 (p) REVERT: A 692 GLN cc_start: 0.8356 (tp40) cc_final: 0.8055 (mm-40) REVERT: B 39 VAL cc_start: 0.5334 (t) cc_final: 0.5056 (m) REVERT: B 122 THR cc_start: 0.6554 (m) cc_final: 0.6331 (p) REVERT: B 427 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5754 (mmm) REVERT: B 440 GLU cc_start: 0.7521 (pm20) cc_final: 0.7055 (mm-30) REVERT: B 460 ASN cc_start: 0.5322 (OUTLIER) cc_final: 0.5048 (p0) REVERT: B 494 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8179 (mm110) REVERT: B 550 MET cc_start: 0.6653 (tpt) cc_final: 0.6203 (ttp) REVERT: B 551 TRP cc_start: 0.5212 (t60) cc_final: 0.4838 (t60) REVERT: B 559 VAL cc_start: 0.8926 (p) cc_final: 0.8588 (t) REVERT: B 599 ARG cc_start: 0.7752 (ptp90) cc_final: 0.7258 (ttp80) REVERT: B 661 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8297 (pp) REVERT: C 39 VAL cc_start: 0.5399 (t) cc_final: 0.5138 (m) REVERT: C 122 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6377 (p) REVERT: C 427 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5815 (mmm) REVERT: C 449 MET cc_start: 0.7782 (tpp) cc_final: 0.6893 (ttm) REVERT: C 492 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8794 (mp) REVERT: C 494 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7974 (mm110) REVERT: C 546 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8392 (tm-30) REVERT: C 561 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: C 599 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7463 (ttp80) REVERT: D 39 VAL cc_start: 0.5376 (t) cc_final: 0.5103 (m) REVERT: D 83 ARG cc_start: 0.5834 (mmt90) cc_final: 0.5392 (mmm-85) REVERT: D 122 THR cc_start: 0.6464 (m) cc_final: 0.6197 (p) REVERT: D 239 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8247 (ptt-90) REVERT: D 427 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5836 (mmm) REVERT: D 442 MET cc_start: 0.7429 (mmp) cc_final: 0.7026 (mmt) REVERT: D 449 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6865 (ttm) REVERT: D 546 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8377 (tm-30) REVERT: D 550 MET cc_start: 0.6699 (tpt) cc_final: 0.6142 (ttp) REVERT: E 39 VAL cc_start: 0.5437 (t) cc_final: 0.5145 (m) REVERT: E 83 ARG cc_start: 0.5842 (mmt90) cc_final: 0.5402 (mmm-85) REVERT: E 122 THR cc_start: 0.6548 (m) cc_final: 0.6329 (p) REVERT: E 427 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5779 (mmm) REVERT: E 440 GLU cc_start: 0.7530 (pm20) cc_final: 0.7058 (mm-30) REVERT: E 449 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7464 (tpp) REVERT: E 460 ASN cc_start: 0.5314 (OUTLIER) cc_final: 0.5006 (p0) REVERT: E 494 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8175 (mm110) REVERT: E 550 MET cc_start: 0.6660 (tpt) cc_final: 0.6199 (ttp) REVERT: E 551 TRP cc_start: 0.5205 (t60) cc_final: 0.4836 (t60) REVERT: E 559 VAL cc_start: 0.8928 (p) cc_final: 0.8595 (t) REVERT: E 599 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7279 (ttp80) REVERT: E 661 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8306 (pp) REVERT: F 39 VAL cc_start: 0.5292 (t) cc_final: 0.5017 (m) REVERT: F 122 THR cc_start: 0.6543 (OUTLIER) cc_final: 0.6309 (p) REVERT: F 427 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5682 (mmm) REVERT: F 492 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8792 (mp) REVERT: F 494 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8191 (mm110) REVERT: F 546 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8367 (tm-30) REVERT: F 550 MET cc_start: 0.6598 (tpt) cc_final: 0.6171 (ttp) REVERT: F 599 ARG cc_start: 0.7817 (ptp90) cc_final: 0.7395 (ttp80) outliers start: 209 outliers final: 150 residues processed: 548 average time/residue: 0.4682 time to fit residues: 412.3671 Evaluate side-chains 545 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 370 time to evaluate : 4.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 416 optimal weight: 5.9990 chunk 260 optimal weight: 0.0470 chunk 253 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 overall best weight: 3.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35130 Z= 0.218 Angle : 0.658 7.916 47514 Z= 0.325 Chirality : 0.046 0.145 5352 Planarity : 0.005 0.046 6234 Dihedral : 8.854 146.265 4926 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.60 % Favored : 92.13 % Rotamer: Outliers : 4.66 % Allowed : 15.32 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.57 (0.13), residues: 4344 helix: -0.68 (0.12), residues: 1746 sheet: -0.87 (0.20), residues: 708 loop : -1.32 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 551 HIS 0.005 0.001 HIS C 317 PHE 0.012 0.001 PHE F 152 TYR 0.013 0.001 TYR A 138 ARG 0.005 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 436 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5433 (t) cc_final: 0.5134 (m) REVERT: A 83 ARG cc_start: 0.5750 (mmt90) cc_final: 0.5532 (mmt90) REVERT: A 122 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.6255 (p) REVERT: A 440 GLU cc_start: 0.7512 (pm20) cc_final: 0.6667 (tp30) REVERT: A 442 MET cc_start: 0.7459 (mmp) cc_final: 0.7055 (mmt) REVERT: A 449 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6862 (ttm) REVERT: A 546 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 550 MET cc_start: 0.6668 (tpt) cc_final: 0.6180 (ttp) REVERT: A 616 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7509 (m-40) REVERT: A 692 GLN cc_start: 0.8291 (tp40) cc_final: 0.8019 (mm110) REVERT: B 39 VAL cc_start: 0.5230 (t) cc_final: 0.4958 (m) REVERT: B 66 GLU cc_start: 0.6775 (mp0) cc_final: 0.5481 (mt-10) REVERT: B 83 ARG cc_start: 0.5844 (mmt90) cc_final: 0.5535 (mmm-85) REVERT: B 427 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5789 (mmm) REVERT: B 440 GLU cc_start: 0.7466 (pm20) cc_final: 0.6687 (tm-30) REVERT: B 449 MET cc_start: 0.7769 (tpp) cc_final: 0.7406 (tpp) REVERT: B 460 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.5016 (p0) REVERT: B 550 MET cc_start: 0.6760 (tpt) cc_final: 0.6290 (ttp) REVERT: B 559 VAL cc_start: 0.8876 (p) cc_final: 0.8555 (t) REVERT: B 561 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: B 599 ARG cc_start: 0.7727 (ptp90) cc_final: 0.7253 (ttp80) REVERT: B 661 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8215 (pp) REVERT: C 39 VAL cc_start: 0.5349 (t) cc_final: 0.5089 (m) REVERT: C 427 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5836 (mmm) REVERT: C 449 MET cc_start: 0.7739 (tpp) cc_final: 0.6873 (ttm) REVERT: C 494 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7984 (mm110) REVERT: C 546 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 550 MET cc_start: 0.6324 (tpt) cc_final: 0.5875 (ptt) REVERT: C 599 ARG cc_start: 0.7757 (ptp90) cc_final: 0.7357 (ttp80) REVERT: D 39 VAL cc_start: 0.5438 (t) cc_final: 0.5138 (m) REVERT: D 83 ARG cc_start: 0.5833 (mmt90) cc_final: 0.5508 (mmm-85) REVERT: D 122 THR cc_start: 0.6408 (OUTLIER) cc_final: 0.6201 (p) REVERT: D 158 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7822 (mtt) REVERT: D 239 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8220 (ptt-90) REVERT: D 427 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5878 (mmm) REVERT: D 440 GLU cc_start: 0.7493 (pm20) cc_final: 0.6655 (tp30) REVERT: D 442 MET cc_start: 0.7478 (mmp) cc_final: 0.7064 (mmt) REVERT: D 449 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6834 (ttm) REVERT: D 546 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 550 MET cc_start: 0.6721 (tpt) cc_final: 0.6025 (ptm) REVERT: D 551 TRP cc_start: 0.4817 (t60) cc_final: 0.4607 (t60) REVERT: D 616 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7508 (m-40) REVERT: E 39 VAL cc_start: 0.5376 (t) cc_final: 0.5098 (m) REVERT: E 66 GLU cc_start: 0.6815 (mp0) cc_final: 0.5547 (mt-10) REVERT: E 83 ARG cc_start: 0.5889 (mmt90) cc_final: 0.5439 (mmm-85) REVERT: E 427 MET cc_start: 0.6183 (OUTLIER) cc_final: 0.5963 (mmm) REVERT: E 440 GLU cc_start: 0.7481 (pm20) cc_final: 0.6708 (tm-30) REVERT: E 449 MET cc_start: 0.7741 (tpp) cc_final: 0.7451 (tpp) REVERT: E 460 ASN cc_start: 0.5272 (OUTLIER) cc_final: 0.5025 (p0) REVERT: E 494 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8175 (mm110) REVERT: E 550 MET cc_start: 0.6754 (tpt) cc_final: 0.6287 (ttp) REVERT: E 551 TRP cc_start: 0.5218 (t60) cc_final: 0.4889 (t60) REVERT: E 559 VAL cc_start: 0.8879 (p) cc_final: 0.8553 (t) REVERT: E 561 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: E 599 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7284 (ttp80) REVERT: F 39 VAL cc_start: 0.5251 (t) cc_final: 0.4997 (m) REVERT: F 66 GLU cc_start: 0.6677 (mp0) cc_final: 0.5763 (pt0) REVERT: F 122 THR cc_start: 0.6534 (OUTLIER) cc_final: 0.6299 (p) REVERT: F 148 LYS cc_start: 0.6537 (mtpp) cc_final: 0.6303 (mtpp) REVERT: F 427 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5767 (mmm) REVERT: F 440 GLU cc_start: 0.7452 (pm20) cc_final: 0.6648 (tm-30) REVERT: F 449 MET cc_start: 0.7590 (tpp) cc_final: 0.6799 (ttm) REVERT: F 494 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8168 (mm110) REVERT: F 546 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8365 (tm-30) REVERT: F 550 MET cc_start: 0.6530 (tpt) cc_final: 0.6163 (ttp) REVERT: F 559 VAL cc_start: 0.8776 (p) cc_final: 0.8394 (t) REVERT: F 599 ARG cc_start: 0.7763 (ptp90) cc_final: 0.7352 (ttp80) outliers start: 173 outliers final: 127 residues processed: 538 average time/residue: 0.4711 time to fit residues: 405.4475 Evaluate side-chains 561 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 412 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 40.0000 chunk 166 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 chunk 283 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN A 692 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35130 Z= 0.221 Angle : 0.650 6.748 47514 Z= 0.320 Chirality : 0.045 0.142 5352 Planarity : 0.005 0.047 6234 Dihedral : 8.765 145.689 4926 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.64 % Favored : 92.08 % Rotamer: Outliers : 4.79 % Allowed : 15.21 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.42 (0.13), residues: 4344 helix: -0.55 (0.12), residues: 1746 sheet: -0.78 (0.20), residues: 708 loop : -1.25 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 551 HIS 0.006 0.001 HIS A 384 PHE 0.012 0.001 PHE C 152 TYR 0.013 0.001 TYR C 173 ARG 0.005 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 424 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5369 (t) cc_final: 0.5101 (m) REVERT: A 66 GLU cc_start: 0.6757 (mp0) cc_final: 0.5613 (mt-10) REVERT: A 122 THR cc_start: 0.6503 (OUTLIER) cc_final: 0.6273 (p) REVERT: A 158 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7826 (mtm) REVERT: A 239 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8060 (ptp90) REVERT: A 442 MET cc_start: 0.7495 (mmp) cc_final: 0.7051 (mmt) REVERT: A 449 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6871 (ttm) REVERT: A 546 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 550 MET cc_start: 0.6797 (tpt) cc_final: 0.6304 (ttp) REVERT: A 551 TRP cc_start: 0.4574 (t60) cc_final: 0.3064 (t-100) REVERT: A 616 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: A 679 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7252 (p) REVERT: A 692 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8041 (mm110) REVERT: B 39 VAL cc_start: 0.5200 (t) cc_final: 0.4924 (m) REVERT: B 66 GLU cc_start: 0.6762 (mp0) cc_final: 0.5566 (mt-10) REVERT: B 83 ARG cc_start: 0.5856 (mmt90) cc_final: 0.5564 (mmm-85) REVERT: B 427 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5808 (mmm) REVERT: B 449 MET cc_start: 0.7794 (tpp) cc_final: 0.7415 (tpp) REVERT: B 460 ASN cc_start: 0.5169 (OUTLIER) cc_final: 0.4893 (p0) REVERT: B 494 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8173 (mm110) REVERT: B 550 MET cc_start: 0.6844 (tpt) cc_final: 0.6113 (ptm) REVERT: B 559 VAL cc_start: 0.8835 (p) cc_final: 0.8513 (t) REVERT: B 561 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: B 599 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7150 (ttp80) REVERT: B 661 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8253 (pp) REVERT: C 39 VAL cc_start: 0.5307 (t) cc_final: 0.5041 (m) REVERT: C 66 GLU cc_start: 0.6814 (mp0) cc_final: 0.5815 (pt0) REVERT: C 427 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5845 (mmm) REVERT: C 440 GLU cc_start: 0.7428 (pm20) cc_final: 0.6567 (tm-30) REVERT: C 449 MET cc_start: 0.7742 (tpp) cc_final: 0.6853 (ttm) REVERT: C 494 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7960 (mm110) REVERT: C 546 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 561 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: C 599 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7347 (ttp80) REVERT: D 39 VAL cc_start: 0.5328 (t) cc_final: 0.5064 (m) REVERT: D 66 GLU cc_start: 0.6720 (mp0) cc_final: 0.5769 (pt0) REVERT: D 83 ARG cc_start: 0.5857 (mmt90) cc_final: 0.5460 (mmm-85) REVERT: D 84 MET cc_start: 0.6847 (mtp) cc_final: 0.6634 (ttp) REVERT: D 122 THR cc_start: 0.6487 (OUTLIER) cc_final: 0.6258 (p) REVERT: D 158 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7825 (mtm) REVERT: D 427 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5890 (mmm) REVERT: D 440 GLU cc_start: 0.7509 (pm20) cc_final: 0.6803 (tp30) REVERT: D 442 MET cc_start: 0.7479 (mmp) cc_final: 0.7056 (mmt) REVERT: D 449 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6864 (ttm) REVERT: D 546 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 550 MET cc_start: 0.6735 (tpt) cc_final: 0.6226 (ttp) REVERT: D 551 TRP cc_start: 0.4767 (t60) cc_final: 0.3267 (t-100) REVERT: D 616 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7552 (m-40) REVERT: D 692 GLN cc_start: 0.7519 (mm110) cc_final: 0.7234 (mm-40) REVERT: E 39 VAL cc_start: 0.5314 (t) cc_final: 0.5044 (m) REVERT: E 66 GLU cc_start: 0.6750 (mp0) cc_final: 0.5573 (mt-10) REVERT: E 83 ARG cc_start: 0.5870 (mmt90) cc_final: 0.5439 (mmm-85) REVERT: E 427 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5969 (mmm) REVERT: E 449 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7457 (tpp) REVERT: E 460 ASN cc_start: 0.5212 (OUTLIER) cc_final: 0.4943 (p0) REVERT: E 550 MET cc_start: 0.6904 (tpt) cc_final: 0.6146 (ptm) REVERT: E 559 VAL cc_start: 0.8838 (p) cc_final: 0.8513 (t) REVERT: E 561 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: E 599 ARG cc_start: 0.7742 (ptp90) cc_final: 0.7298 (ttp80) REVERT: E 661 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8228 (pp) REVERT: F 39 VAL cc_start: 0.5213 (t) cc_final: 0.4970 (m) REVERT: F 66 GLU cc_start: 0.6581 (mp0) cc_final: 0.5772 (pt0) REVERT: F 122 THR cc_start: 0.6580 (OUTLIER) cc_final: 0.6358 (p) REVERT: F 427 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5806 (mmm) REVERT: F 440 GLU cc_start: 0.7453 (pm20) cc_final: 0.6563 (tm-30) REVERT: F 449 MET cc_start: 0.7708 (tpp) cc_final: 0.6806 (ttm) REVERT: F 494 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8192 (mm110) REVERT: F 546 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8385 (tm-30) REVERT: F 550 MET cc_start: 0.6562 (tpt) cc_final: 0.6189 (ttp) REVERT: F 559 VAL cc_start: 0.8725 (p) cc_final: 0.8379 (t) REVERT: F 599 ARG cc_start: 0.7770 (ptp90) cc_final: 0.7368 (ttp80) outliers start: 178 outliers final: 136 residues processed: 535 average time/residue: 0.4627 time to fit residues: 395.0661 Evaluate side-chains 579 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 415 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 0.0670 chunk 398 optimal weight: 0.8980 chunk 363 optimal weight: 30.0000 chunk 388 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 304 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35130 Z= 0.208 Angle : 0.643 6.858 47514 Z= 0.317 Chirality : 0.045 0.139 5352 Planarity : 0.005 0.047 6234 Dihedral : 8.697 144.830 4926 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.18 % Favored : 92.54 % Rotamer: Outliers : 4.87 % Allowed : 15.21 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.34 (0.13), residues: 4344 helix: -0.49 (0.12), residues: 1746 sheet: -0.72 (0.20), residues: 708 loop : -1.20 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 551 HIS 0.004 0.001 HIS A 384 PHE 0.012 0.001 PHE F 152 TYR 0.013 0.001 TYR D 138 ARG 0.012 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 433 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5308 (t) cc_final: 0.5049 (m) REVERT: A 66 GLU cc_start: 0.6695 (mp0) cc_final: 0.5810 (pt0) REVERT: A 122 THR cc_start: 0.6506 (OUTLIER) cc_final: 0.6280 (p) REVERT: A 158 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: A 239 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8136 (ptp90) REVERT: A 440 GLU cc_start: 0.7617 (pm20) cc_final: 0.6796 (tm-30) REVERT: A 442 MET cc_start: 0.7444 (mmp) cc_final: 0.7050 (mmt) REVERT: A 449 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6885 (ttm) REVERT: A 546 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 550 MET cc_start: 0.6708 (tpt) cc_final: 0.6294 (ttp) REVERT: A 551 TRP cc_start: 0.4532 (t60) cc_final: 0.4318 (t60) REVERT: A 679 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7250 (p) REVERT: A 692 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8091 (mm110) REVERT: B 39 VAL cc_start: 0.5203 (t) cc_final: 0.4935 (m) REVERT: B 66 GLU cc_start: 0.6724 (mp0) cc_final: 0.5559 (mt-10) REVERT: B 83 ARG cc_start: 0.5890 (mmt90) cc_final: 0.5595 (mmm-85) REVERT: B 449 MET cc_start: 0.7784 (tpp) cc_final: 0.7400 (tpp) REVERT: B 460 ASN cc_start: 0.5133 (OUTLIER) cc_final: 0.4873 (p0) REVERT: B 494 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8161 (mm110) REVERT: B 550 MET cc_start: 0.6950 (tpt) cc_final: 0.6193 (ptm) REVERT: B 551 TRP cc_start: 0.4972 (t60) cc_final: 0.4615 (t60) REVERT: B 559 VAL cc_start: 0.8812 (p) cc_final: 0.8466 (t) REVERT: B 561 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: B 599 ARG cc_start: 0.7707 (ptp90) cc_final: 0.7226 (ttp80) REVERT: B 661 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8267 (pp) REVERT: C 39 VAL cc_start: 0.5258 (t) cc_final: 0.5037 (m) REVERT: C 427 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5838 (mmm) REVERT: C 440 GLU cc_start: 0.7369 (pm20) cc_final: 0.6505 (tm-30) REVERT: C 449 MET cc_start: 0.7738 (tpp) cc_final: 0.6855 (ttm) REVERT: C 494 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7958 (mm110) REVERT: C 546 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8388 (tm-30) REVERT: C 550 MET cc_start: 0.6463 (tpt) cc_final: 0.5992 (ptt) REVERT: C 561 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: C 599 ARG cc_start: 0.7705 (ptp90) cc_final: 0.7295 (ttp80) REVERT: C 692 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7465 (tp40) REVERT: D 39 VAL cc_start: 0.5290 (t) cc_final: 0.5045 (m) REVERT: D 66 GLU cc_start: 0.6636 (mp0) cc_final: 0.6015 (mm-30) REVERT: D 83 ARG cc_start: 0.5856 (mmt90) cc_final: 0.5505 (mmm-85) REVERT: D 122 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.6272 (p) REVERT: D 158 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: D 239 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8037 (ptp90) REVERT: D 440 GLU cc_start: 0.7611 (pm20) cc_final: 0.6784 (tm-30) REVERT: D 442 MET cc_start: 0.7453 (mmp) cc_final: 0.7092 (mmt) REVERT: D 449 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6851 (ttm) REVERT: D 546 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 550 MET cc_start: 0.6754 (tpt) cc_final: 0.6318 (ttp) REVERT: D 551 TRP cc_start: 0.4747 (t60) cc_final: 0.3289 (t-100) REVERT: D 692 GLN cc_start: 0.7492 (mm110) cc_final: 0.7222 (mm-40) REVERT: E 39 VAL cc_start: 0.5291 (t) cc_final: 0.5029 (m) REVERT: E 66 GLU cc_start: 0.6728 (mp0) cc_final: 0.5613 (mt-10) REVERT: E 83 ARG cc_start: 0.5906 (mmt90) cc_final: 0.5458 (mmm-85) REVERT: E 427 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5963 (mmm) REVERT: E 449 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7426 (tpp) REVERT: E 460 ASN cc_start: 0.5143 (OUTLIER) cc_final: 0.4875 (p0) REVERT: E 494 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (mm110) REVERT: E 550 MET cc_start: 0.6877 (tpt) cc_final: 0.6171 (ptm) REVERT: E 559 VAL cc_start: 0.8808 (p) cc_final: 0.8459 (t) REVERT: E 561 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: E 599 ARG cc_start: 0.7762 (ptp90) cc_final: 0.7194 (ttp80) REVERT: E 661 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8266 (pp) REVERT: F 39 VAL cc_start: 0.5151 (t) cc_final: 0.4913 (m) REVERT: F 66 GLU cc_start: 0.6614 (mp0) cc_final: 0.5753 (pt0) REVERT: F 122 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6352 (p) REVERT: F 427 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5813 (mmm) REVERT: F 440 GLU cc_start: 0.7425 (pm20) cc_final: 0.6600 (tm-30) REVERT: F 449 MET cc_start: 0.7669 (tpp) cc_final: 0.6793 (ttm) REVERT: F 494 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8191 (mm110) REVERT: F 546 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8406 (tm-30) REVERT: F 550 MET cc_start: 0.6625 (tpt) cc_final: 0.6286 (ttp) REVERT: F 561 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: F 599 ARG cc_start: 0.7707 (ptp90) cc_final: 0.7286 (ttp80) REVERT: F 692 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7482 (tp40) outliers start: 181 outliers final: 134 residues processed: 546 average time/residue: 0.4659 time to fit residues: 409.1115 Evaluate side-chains 586 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 423 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.4980 chunk 410 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 430 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35130 Z= 0.198 Angle : 0.638 7.084 47514 Z= 0.314 Chirality : 0.045 0.255 5352 Planarity : 0.005 0.048 6234 Dihedral : 8.619 144.094 4926 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.62 % Favored : 92.10 % Rotamer: Outliers : 4.39 % Allowed : 15.72 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 4344 helix: -0.43 (0.13), residues: 1746 sheet: -0.67 (0.20), residues: 708 loop : -1.16 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 551 HIS 0.004 0.001 HIS A 384 PHE 0.012 0.001 PHE C 152 TYR 0.013 0.001 TYR B 173 ARG 0.010 0.000 ARG A 693 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 429 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.5284 (t) cc_final: 0.5036 (m) REVERT: A 66 GLU cc_start: 0.6630 (mp0) cc_final: 0.5818 (pt0) REVERT: A 122 THR cc_start: 0.6526 (OUTLIER) cc_final: 0.6298 (p) REVERT: A 158 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7844 (mtm) REVERT: A 162 GLU cc_start: 0.6573 (tt0) cc_final: 0.6368 (tt0) REVERT: A 239 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8189 (ptp90) REVERT: A 440 GLU cc_start: 0.7538 (pm20) cc_final: 0.6785 (tm-30) REVERT: A 442 MET cc_start: 0.7459 (mmp) cc_final: 0.6988 (mmt) REVERT: A 449 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.6878 (ttm) REVERT: A 546 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 550 MET cc_start: 0.6777 (tpt) cc_final: 0.6348 (ttp) REVERT: A 551 TRP cc_start: 0.4506 (t60) cc_final: 0.4276 (t60) REVERT: A 679 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7221 (p) REVERT: A 692 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: B 39 VAL cc_start: 0.5182 (t) cc_final: 0.4913 (m) REVERT: B 66 GLU cc_start: 0.6710 (mp0) cc_final: 0.5598 (mt-10) REVERT: B 83 ARG cc_start: 0.5889 (mmt90) cc_final: 0.5608 (mmm-85) REVERT: B 449 MET cc_start: 0.7777 (tpp) cc_final: 0.7370 (tpp) REVERT: B 460 ASN cc_start: 0.5120 (OUTLIER) cc_final: 0.4866 (p0) REVERT: B 494 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (mm110) REVERT: B 550 MET cc_start: 0.6976 (tpt) cc_final: 0.6228 (ptm) REVERT: B 551 TRP cc_start: 0.4940 (t60) cc_final: 0.4425 (t60) REVERT: B 559 VAL cc_start: 0.8784 (p) cc_final: 0.8452 (t) REVERT: B 561 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 599 ARG cc_start: 0.7724 (ptp90) cc_final: 0.7275 (ttp80) REVERT: B 661 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8272 (pp) REVERT: C 39 VAL cc_start: 0.5277 (t) cc_final: 0.5033 (m) REVERT: C 66 GLU cc_start: 0.6746 (mp0) cc_final: 0.6161 (mm-30) REVERT: C 427 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5811 (mmm) REVERT: C 440 GLU cc_start: 0.7359 (pm20) cc_final: 0.6701 (tm-30) REVERT: C 449 MET cc_start: 0.7719 (tpp) cc_final: 0.6843 (ttm) REVERT: C 494 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7965 (mm110) REVERT: C 546 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 550 MET cc_start: 0.6434 (tpt) cc_final: 0.5766 (ptm) REVERT: C 559 VAL cc_start: 0.8971 (p) cc_final: 0.8710 (t) REVERT: C 599 ARG cc_start: 0.7665 (ptp90) cc_final: 0.7233 (ttp80) REVERT: C 692 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7394 (tp40) REVERT: D 39 VAL cc_start: 0.5324 (t) cc_final: 0.5049 (m) REVERT: D 66 GLU cc_start: 0.6568 (mp0) cc_final: 0.5494 (mt-10) REVERT: D 83 ARG cc_start: 0.5816 (mmt90) cc_final: 0.5560 (mmm-85) REVERT: D 122 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6276 (p) REVERT: D 158 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7843 (mtm) REVERT: D 239 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8072 (ptp90) REVERT: D 440 GLU cc_start: 0.7550 (pm20) cc_final: 0.6770 (tm-30) REVERT: D 442 MET cc_start: 0.7461 (mmp) cc_final: 0.7027 (mmt) REVERT: D 449 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6860 (ttm) REVERT: D 546 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 550 MET cc_start: 0.6709 (tpt) cc_final: 0.6304 (ttp) REVERT: D 551 TRP cc_start: 0.4638 (t60) cc_final: 0.3187 (t-100) REVERT: D 692 GLN cc_start: 0.7407 (mm110) cc_final: 0.7147 (mm-40) REVERT: E 39 VAL cc_start: 0.5293 (t) cc_final: 0.5029 (m) REVERT: E 66 GLU cc_start: 0.6697 (mp0) cc_final: 0.6172 (mm-30) REVERT: E 83 ARG cc_start: 0.5890 (mmt90) cc_final: 0.5438 (mmm-85) REVERT: E 449 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7421 (tpp) REVERT: E 460 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4867 (p0) REVERT: E 494 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (mm110) REVERT: E 550 MET cc_start: 0.6943 (tpt) cc_final: 0.6196 (ptm) REVERT: E 551 TRP cc_start: 0.4968 (t60) cc_final: 0.4477 (t60) REVERT: E 559 VAL cc_start: 0.8782 (p) cc_final: 0.8448 (t) REVERT: E 561 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: E 599 ARG cc_start: 0.7720 (ptp90) cc_final: 0.7244 (ttp80) REVERT: E 661 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8270 (pp) REVERT: F 39 VAL cc_start: 0.5192 (t) cc_final: 0.4965 (m) REVERT: F 66 GLU cc_start: 0.6569 (mp0) cc_final: 0.5641 (pt0) REVERT: F 122 THR cc_start: 0.6586 (OUTLIER) cc_final: 0.6353 (p) REVERT: F 427 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5818 (mmm) REVERT: F 440 GLU cc_start: 0.7458 (pm20) cc_final: 0.6685 (tm-30) REVERT: F 449 MET cc_start: 0.7698 (tpp) cc_final: 0.6823 (ttm) REVERT: F 494 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8161 (mm110) REVERT: F 546 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8384 (tm-30) REVERT: F 550 MET cc_start: 0.6629 (tpt) cc_final: 0.6277 (ttp) REVERT: F 561 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: F 599 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7302 (ttp80) REVERT: F 692 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7393 (tp40) outliers start: 163 outliers final: 121 residues processed: 529 average time/residue: 0.4876 time to fit residues: 415.4309 Evaluate side-chains 570 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 422 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 449 MET Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 701 GLU Chi-restraints excluded: chain E residue 746 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 697 LEU Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 352 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN C 36 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113142 restraints weight = 58544.781| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.87 r_work: 0.3309 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35130 Z= 0.268 Angle : 0.672 6.941 47514 Z= 0.332 Chirality : 0.047 0.281 5352 Planarity : 0.005 0.047 6234 Dihedral : 8.777 146.851 4926 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.73 % Favored : 91.99 % Rotamer: Outliers : 4.82 % Allowed : 15.48 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.35 (0.13), residues: 4344 helix: -0.52 (0.12), residues: 1746 sheet: -0.64 (0.21), residues: 672 loop : -1.22 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 551 HIS 0.006 0.001 HIS A 384 PHE 0.013 0.002 PHE D 576 TYR 0.014 0.002 TYR D 138 ARG 0.010 0.000 ARG A 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8270.23 seconds wall clock time: 148 minutes 48.79 seconds (8928.79 seconds total)