Starting phenix.real_space_refine on Mon Apr 8 07:45:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/04_2024/8ona_16984_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/04_2024/8ona_16984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/04_2024/8ona_16984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/04_2024/8ona_16984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/04_2024/8ona_16984_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/04_2024/8ona_16984_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8217 2.51 5 N 2154 2.21 5 O 2421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 274": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12900 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4188 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 29, 'TRANS': 493} Chain breaks: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 3} Chain: "B" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4188 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 29, 'TRANS': 493} Chain breaks: 1 Chain: "C" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4188 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 29, 'TRANS': 493} Chain breaks: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 3} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 3} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.34, per 1000 atoms: 0.57 Number of scatterers: 12900 At special positions: 0 Unit cell: (107.31, 104.244, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2421 8.00 N 2154 7.00 C 8217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 180 " " NAG A 602 " - " ASN A 299 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 444 " " NAG A 605 " - " ASN A 460 " " NAG B 601 " - " ASN B 180 " " NAG B 602 " - " ASN B 299 " " NAG B 603 " - " ASN B 392 " " NAG B 604 " - " ASN B 444 " " NAG B 605 " - " ASN B 460 " " NAG C 601 " - " ASN C 180 " " NAG C 602 " - " ASN C 299 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 444 " " NAG C 605 " - " ASN C 460 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 9 sheets defined 44.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 17 through 23 removed outlier: 4.449A pdb=" N LYS A 21 " --> pdb=" O HIS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 57 Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.663A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.184A pdb=" N LEU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 315 through 331 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 366 through 391 removed outlier: 4.224A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.641A pdb=" N CYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.665A pdb=" N PHE A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 removed outlier: 4.207A pdb=" N GLN A 449 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY A 450 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 removed outlier: 5.673A pdb=" N GLU A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 513 through 528 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 17 through 23 removed outlier: 4.450A pdb=" N LYS B 21 " --> pdb=" O HIS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 57 Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.663A pdb=" N LYS B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.185A pdb=" N LEU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 315 through 331 Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 358 through 361 Processing helix chain 'B' and resid 366 through 391 removed outlier: 4.224A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.641A pdb=" N CYS B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.665A pdb=" N PHE B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 4.207A pdb=" N GLN B 449 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 450 " --> pdb=" O GLY B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 470 removed outlier: 5.673A pdb=" N GLU B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 513 through 528 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 17 through 23 removed outlier: 4.450A pdb=" N LYS C 21 " --> pdb=" O HIS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 57 Processing helix chain 'C' and resid 87 through 99 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 113 through 132 removed outlier: 3.663A pdb=" N LYS C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Proline residue: C 127 - end of helix Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.185A pdb=" N LEU C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 358 through 361 Processing helix chain 'C' and resid 366 through 391 removed outlier: 4.224A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.641A pdb=" N CYS C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.665A pdb=" N PHE C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 458 removed outlier: 4.207A pdb=" N GLN C 449 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY C 450 " --> pdb=" O GLY C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 removed outlier: 5.673A pdb=" N GLU C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET C 468 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 Processing helix chain 'C' and resid 513 through 528 Processing sheet with id= A, first strand: chain 'A' and resid 61 through 68 Processing sheet with id= B, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.458A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 416 through 418 removed outlier: 7.353A pdb=" N PHE A 471 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ALA A 281 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG A 473 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE A 283 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 475 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 285 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 477 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 224 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 169 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 61 through 68 Processing sheet with id= E, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.457A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 416 through 418 removed outlier: 7.353A pdb=" N PHE B 471 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ALA B 281 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 473 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE B 283 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 475 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE B 285 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 477 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 224 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 169 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 61 through 68 Processing sheet with id= H, first strand: chain 'C' and resid 185 through 189 removed outlier: 6.458A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 416 through 418 removed outlier: 7.353A pdb=" N PHE C 471 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ALA C 281 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG C 473 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE C 283 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN C 475 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE C 285 " --> pdb=" O ASN C 475 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR C 477 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU C 224 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL C 169 " --> pdb=" O LEU C 224 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3179 1.33 - 1.45: 2854 1.45 - 1.58: 7035 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 13230 Sorted by residual: bond pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.18e-02 7.18e+03 1.65e+01 bond pdb=" N GLN C 13 " pdb=" CA GLN C 13 " ideal model delta sigma weight residual 1.456 1.503 -0.048 1.18e-02 7.18e+03 1.62e+01 bond pdb=" N GLN A 13 " pdb=" CA GLN A 13 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.18e-02 7.18e+03 1.61e+01 bond pdb=" C ASP A 5 " pdb=" O ASP A 5 " ideal model delta sigma weight residual 1.235 1.277 -0.042 1.26e-02 6.30e+03 1.10e+01 bond pdb=" C ASP B 5 " pdb=" O ASP B 5 " ideal model delta sigma weight residual 1.235 1.277 -0.041 1.26e-02 6.30e+03 1.07e+01 ... (remaining 13225 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.66: 462 106.66 - 113.52: 7011 113.52 - 120.38: 5185 120.38 - 127.24: 5099 127.24 - 134.10: 159 Bond angle restraints: 17916 Sorted by residual: angle pdb=" C GLU C 12 " pdb=" N GLN C 13 " pdb=" CA GLN C 13 " ideal model delta sigma weight residual 122.73 113.82 8.91 1.61e+00 3.86e-01 3.06e+01 angle pdb=" C GLU B 12 " pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 122.73 113.83 8.90 1.61e+00 3.86e-01 3.05e+01 angle pdb=" C GLU A 12 " pdb=" N GLN A 13 " pdb=" CA GLN A 13 " ideal model delta sigma weight residual 122.73 113.86 8.87 1.61e+00 3.86e-01 3.03e+01 angle pdb=" C GLN C 13 " pdb=" N THR C 14 " pdb=" CA THR C 14 " ideal model delta sigma weight residual 122.64 113.60 9.04 1.70e+00 3.46e-01 2.83e+01 angle pdb=" C GLN A 13 " pdb=" N THR A 14 " pdb=" CA THR A 14 " ideal model delta sigma weight residual 122.64 113.62 9.02 1.70e+00 3.46e-01 2.81e+01 ... (remaining 17911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 7277 15.80 - 31.59: 694 31.59 - 47.39: 150 47.39 - 63.18: 27 63.18 - 78.98: 21 Dihedral angle restraints: 8169 sinusoidal: 3540 harmonic: 4629 Sorted by residual: dihedral pdb=" CA MET A 16 " pdb=" C MET A 16 " pdb=" N HIS A 17 " pdb=" CA HIS A 17 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET B 16 " pdb=" C MET B 16 " pdb=" N HIS B 17 " pdb=" CA HIS B 17 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET C 16 " pdb=" C MET C 16 " pdb=" N HIS C 17 " pdb=" CA HIS C 17 " ideal model delta harmonic sigma weight residual 180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 8166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1733 0.081 - 0.162: 199 0.162 - 0.243: 9 0.243 - 0.324: 3 0.324 - 0.404: 6 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA ARG C 102 " pdb=" N ARG C 102 " pdb=" C ARG C 102 " pdb=" CB ARG C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ARG B 102 " pdb=" N ARG B 102 " pdb=" C ARG B 102 " pdb=" CB ARG B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 1947 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 248 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C ALA C 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA C 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL C 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 248 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ALA A 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA A 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 248 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C ALA B 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA B 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL B 249 " -0.017 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4326 2.84 - 3.35: 12248 3.35 - 3.87: 21542 3.87 - 4.38: 25172 4.38 - 4.90: 42554 Nonbonded interactions: 105842 Sorted by model distance: nonbonded pdb=" O PRO C 20 " pdb=" OD1 ASN C 24 " model vdw 2.322 3.040 nonbonded pdb=" O PRO B 20 " pdb=" OD1 ASN B 24 " model vdw 2.322 3.040 nonbonded pdb=" O PRO A 20 " pdb=" OD1 ASN A 24 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN A 48 " pdb=" OE1 GLN A 504 " model vdw 2.361 3.040 nonbonded pdb=" OE1 GLN C 48 " pdb=" OE1 GLN C 504 " model vdw 2.362 3.040 ... (remaining 105837 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' } ncs_group { reference = 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.880 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.840 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.004 0.051 13230 Z= 0.288 Angle : 0.739 9.037 17916 Z= 0.435 Chirality : 0.052 0.404 1950 Planarity : 0.004 0.029 2310 Dihedral : 13.104 78.976 5109 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.43 % Allowed : 7.49 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1563 helix: 0.16 (0.19), residues: 684 sheet: 1.09 (0.30), residues: 279 loop : 0.59 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 34 HIS 0.005 0.001 HIS B 376 PHE 0.024 0.001 PHE A 33 TYR 0.014 0.002 TYR B 414 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 493 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7599 (ttt) cc_final: 0.7225 (ttt) REVERT: A 49 MET cc_start: 0.6342 (ttt) cc_final: 0.6038 (ttp) REVERT: A 61 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7667 (ttmm) REVERT: A 100 ASP cc_start: 0.7278 (t0) cc_final: 0.6722 (t0) REVERT: A 111 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 120 LYS cc_start: 0.7799 (mttt) cc_final: 0.7550 (tppp) REVERT: A 138 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 203 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 232 LYS cc_start: 0.8380 (mttt) cc_final: 0.8086 (mttm) REVERT: A 271 GLU cc_start: 0.7437 (pt0) cc_final: 0.7225 (pt0) REVERT: A 288 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6768 (mtm-85) REVERT: A 290 ASN cc_start: 0.7792 (m110) cc_final: 0.7591 (m-40) REVERT: A 302 ASP cc_start: 0.7303 (p0) cc_final: 0.6937 (p0) REVERT: A 303 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7370 (mtmt) REVERT: A 380 LYS cc_start: 0.6968 (mtpt) cc_final: 0.6720 (mtpt) REVERT: A 388 LYS cc_start: 0.7247 (mtpp) cc_final: 0.7018 (mtpp) REVERT: A 409 SER cc_start: 0.7501 (m) cc_final: 0.7062 (t) REVERT: A 411 ASP cc_start: 0.7684 (m-30) cc_final: 0.7285 (m-30) REVERT: A 438 LYS cc_start: 0.8094 (mttt) cc_final: 0.7818 (mttp) REVERT: A 440 ASN cc_start: 0.7226 (p0) cc_final: 0.6602 (t0) REVERT: A 465 GLU cc_start: 0.7711 (tp30) cc_final: 0.7496 (tp30) REVERT: A 470 ASP cc_start: 0.7746 (m-30) cc_final: 0.7252 (m-30) REVERT: B 10 PHE cc_start: 0.6376 (t80) cc_final: 0.6023 (t80) REVERT: B 21 LYS cc_start: 0.7265 (tppp) cc_final: 0.6955 (mmtt) REVERT: B 33 PHE cc_start: 0.7398 (t80) cc_final: 0.7149 (t80) REVERT: B 44 MET cc_start: 0.7439 (ttt) cc_final: 0.6852 (ttt) REVERT: B 60 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7633 (Cg_exo) REVERT: B 61 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7513 (mtpp) REVERT: B 62 LYS cc_start: 0.6305 (ttpp) cc_final: 0.6079 (tttp) REVERT: B 100 ASP cc_start: 0.7176 (t0) cc_final: 0.6607 (t70) REVERT: B 135 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 138 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7296 (mp0) REVERT: B 141 GLN cc_start: 0.8124 (mm110) cc_final: 0.7877 (mm110) REVERT: B 156 GLU cc_start: 0.7726 (tt0) cc_final: 0.7498 (tt0) REVERT: B 171 ASN cc_start: 0.8276 (t0) cc_final: 0.8056 (m-40) REVERT: B 203 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 232 LYS cc_start: 0.8211 (mttt) cc_final: 0.7902 (mttp) REVERT: B 244 GLU cc_start: 0.7871 (tp30) cc_final: 0.7668 (tp30) REVERT: B 288 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6751 (mtm110) REVERT: B 301 SER cc_start: 0.6940 (t) cc_final: 0.6600 (p) REVERT: B 303 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7312 (mtpp) REVERT: B 308 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (p0) REVERT: B 310 THR cc_start: 0.8384 (p) cc_final: 0.7780 (t) REVERT: B 311 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6481 (mm-30) REVERT: B 329 GLU cc_start: 0.7453 (tt0) cc_final: 0.7140 (tt0) REVERT: B 353 ASP cc_start: 0.7528 (p0) cc_final: 0.7230 (p0) REVERT: B 380 LYS cc_start: 0.7046 (mtpt) cc_final: 0.6841 (mtpt) REVERT: B 402 PHE cc_start: 0.7967 (m-80) cc_final: 0.7636 (m-80) REVERT: B 425 GLU cc_start: 0.7451 (tp30) cc_final: 0.7138 (mm-30) REVERT: B 440 ASN cc_start: 0.7348 (p0) cc_final: 0.7120 (m-40) REVERT: B 462 SER cc_start: 0.8231 (m) cc_final: 0.7773 (p) REVERT: B 465 GLU cc_start: 0.7664 (tp30) cc_final: 0.7462 (tp30) REVERT: B 466 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 492 TYR cc_start: 0.7852 (t80) cc_final: 0.7159 (t80) REVERT: B 518 GLU cc_start: 0.7175 (tp30) cc_final: 0.6958 (tp30) REVERT: C 7 MET cc_start: 0.6814 (ttm) cc_final: 0.6596 (ttm) REVERT: C 10 PHE cc_start: 0.6183 (t80) cc_final: 0.5851 (t80) REVERT: C 33 PHE cc_start: 0.7353 (t80) cc_final: 0.7052 (t80) REVERT: C 61 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7547 (ttmm) REVERT: C 66 GLU cc_start: 0.7472 (pt0) cc_final: 0.6812 (pm20) REVERT: C 99 GLU cc_start: 0.7502 (tt0) cc_final: 0.7237 (tt0) REVERT: C 100 ASP cc_start: 0.7379 (t0) cc_final: 0.6845 (t70) REVERT: C 120 LYS cc_start: 0.7695 (mttt) cc_final: 0.7408 (ttmm) REVERT: C 138 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7464 (mp0) REVERT: C 142 GLU cc_start: 0.7499 (tt0) cc_final: 0.7223 (tt0) REVERT: C 156 GLU cc_start: 0.7688 (tt0) cc_final: 0.7267 (pm20) REVERT: C 178 ARG cc_start: 0.7384 (ttm170) cc_final: 0.7000 (ttp-170) REVERT: C 181 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7236 (mtpp) REVERT: C 232 LYS cc_start: 0.8394 (mttt) cc_final: 0.8033 (mttp) REVERT: C 249 VAL cc_start: 0.8242 (m) cc_final: 0.8012 (m) REVERT: C 288 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6772 (mtm110) REVERT: C 303 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7369 (mtmt) REVERT: C 346 ASN cc_start: 0.7610 (m-40) cc_final: 0.7362 (m-40) REVERT: C 441 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7062 (mm-30) REVERT: C 462 SER cc_start: 0.8179 (m) cc_final: 0.7817 (t) REVERT: C 463 ASN cc_start: 0.7933 (t0) cc_final: 0.7243 (t0) REVERT: C 465 GLU cc_start: 0.7788 (tp30) cc_final: 0.7518 (tp30) REVERT: C 466 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 470 ASP cc_start: 0.7767 (m-30) cc_final: 0.7556 (m-30) REVERT: C 480 ASP cc_start: 0.7265 (m-30) cc_final: 0.6881 (m-30) REVERT: C 487 GLN cc_start: 0.7708 (tt0) cc_final: 0.7374 (tt0) REVERT: C 492 TYR cc_start: 0.7659 (t80) cc_final: 0.6990 (t80) REVERT: C 494 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6553 (ttp-110) outliers start: 6 outliers final: 0 residues processed: 496 average time/residue: 1.4747 time to fit residues: 786.5052 Evaluate side-chains 396 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 ASN A 297 HIS A 463 ASN A 504 GLN B 324 GLN B 463 ASN B 496 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN C 91 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN C 297 HIS C 319 GLN C 463 ASN C 482 ASN C 496 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 13230 Z= 0.316 Angle : 0.676 16.305 17916 Z= 0.344 Chirality : 0.046 0.265 1950 Planarity : 0.005 0.038 2310 Dihedral : 5.317 36.254 2040 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.50 % Allowed : 14.13 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1563 helix: 0.83 (0.20), residues: 675 sheet: 1.09 (0.28), residues: 279 loop : 0.41 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 349 HIS 0.006 0.001 HIS B 260 PHE 0.020 0.002 PHE B 431 TYR 0.018 0.002 TYR A 414 ARG 0.007 0.001 ARG C 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 429 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7575 (ttp) cc_final: 0.7098 (ptp) REVERT: A 44 MET cc_start: 0.7581 (ttt) cc_final: 0.7219 (ttt) REVERT: A 49 MET cc_start: 0.6360 (ttt) cc_final: 0.6078 (ttp) REVERT: A 61 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7703 (ttmm) REVERT: A 62 LYS cc_start: 0.6579 (ttpp) cc_final: 0.6378 (tttp) REVERT: A 100 ASP cc_start: 0.7199 (t0) cc_final: 0.6669 (t0) REVERT: A 203 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 232 LYS cc_start: 0.8441 (mttt) cc_final: 0.8167 (mttm) REVERT: A 273 TYR cc_start: 0.8240 (m-80) cc_final: 0.8029 (m-80) REVERT: A 288 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7037 (mtm-85) REVERT: A 301 SER cc_start: 0.7453 (t) cc_final: 0.6668 (p) REVERT: A 302 ASP cc_start: 0.7295 (p0) cc_final: 0.7033 (p0) REVERT: A 336 VAL cc_start: 0.7857 (p) cc_final: 0.7589 (t) REVERT: A 363 THR cc_start: 0.7667 (m) cc_final: 0.7282 (t) REVERT: A 380 LYS cc_start: 0.6889 (mtpt) cc_final: 0.6672 (mtpt) REVERT: A 407 GLU cc_start: 0.7407 (tt0) cc_final: 0.7166 (tt0) REVERT: A 411 ASP cc_start: 0.7741 (m-30) cc_final: 0.7532 (m-30) REVERT: A 438 LYS cc_start: 0.8165 (mttt) cc_final: 0.7883 (mttm) REVERT: A 465 GLU cc_start: 0.7702 (tp30) cc_final: 0.7473 (tp30) REVERT: A 470 ASP cc_start: 0.7726 (m-30) cc_final: 0.7293 (m-30) REVERT: A 487 GLN cc_start: 0.7680 (tt0) cc_final: 0.7246 (tt0) REVERT: A 521 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 33 PHE cc_start: 0.7427 (t80) cc_final: 0.7167 (t80) REVERT: B 44 MET cc_start: 0.7405 (ttt) cc_final: 0.6820 (ttt) REVERT: B 49 MET cc_start: 0.6398 (ttt) cc_final: 0.5682 (tmm) REVERT: B 51 GLU cc_start: 0.6573 (tp30) cc_final: 0.6360 (tp30) REVERT: B 61 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7605 (ttpp) REVERT: B 66 GLU cc_start: 0.7640 (pt0) cc_final: 0.7180 (pm20) REVERT: B 121 LYS cc_start: 0.7704 (ttpp) cc_final: 0.7503 (tttm) REVERT: B 135 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 156 GLU cc_start: 0.7721 (tt0) cc_final: 0.7332 (tt0) REVERT: B 203 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7311 (mm-30) REVERT: B 232 LYS cc_start: 0.8225 (mttt) cc_final: 0.7930 (mttp) REVERT: B 244 GLU cc_start: 0.7802 (tp30) cc_final: 0.7325 (tp30) REVERT: B 288 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7082 (mtm-85) REVERT: B 303 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7509 (mtpp) REVERT: B 310 THR cc_start: 0.8387 (p) cc_final: 0.7853 (t) REVERT: B 311 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6446 (mm-30) REVERT: B 329 GLU cc_start: 0.7457 (tt0) cc_final: 0.7153 (tt0) REVERT: B 363 THR cc_start: 0.7649 (m) cc_final: 0.7217 (t) REVERT: B 370 GLN cc_start: 0.7214 (mt0) cc_final: 0.6745 (mm110) REVERT: B 463 ASN cc_start: 0.7825 (t0) cc_final: 0.7320 (t0) REVERT: B 465 GLU cc_start: 0.7699 (tp30) cc_final: 0.7469 (tp30) REVERT: B 466 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6727 (mm-30) REVERT: B 492 TYR cc_start: 0.8008 (t80) cc_final: 0.7358 (t80) REVERT: B 518 GLU cc_start: 0.7213 (tp30) cc_final: 0.7005 (tp30) REVERT: B 521 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 7 MET cc_start: 0.6937 (ttm) cc_final: 0.6712 (ttm) REVERT: C 33 PHE cc_start: 0.7365 (t80) cc_final: 0.6994 (t80) REVERT: C 44 MET cc_start: 0.7454 (ttt) cc_final: 0.7192 (ttt) REVERT: C 51 GLU cc_start: 0.6850 (tp30) cc_final: 0.6536 (tm-30) REVERT: C 61 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7383 (mtpm) REVERT: C 62 LYS cc_start: 0.6577 (ttpp) cc_final: 0.6186 (ttmm) REVERT: C 66 GLU cc_start: 0.7522 (pt0) cc_final: 0.7308 (pt0) REVERT: C 99 GLU cc_start: 0.7475 (tt0) cc_final: 0.7235 (tt0) REVERT: C 120 LYS cc_start: 0.7737 (mttt) cc_final: 0.7506 (ttmm) REVERT: C 156 GLU cc_start: 0.7705 (tt0) cc_final: 0.7337 (tt0) REVERT: C 232 LYS cc_start: 0.8417 (mttt) cc_final: 0.8052 (mttp) REVERT: C 288 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6991 (mtm-85) REVERT: C 301 SER cc_start: 0.7432 (t) cc_final: 0.6866 (p) REVERT: C 312 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7770 (ttp-170) REVERT: C 346 ASN cc_start: 0.7700 (m-40) cc_final: 0.7433 (m-40) REVERT: C 355 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7272 (p0) REVERT: C 366 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6651 (mt-10) REVERT: C 380 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6865 (mmmm) REVERT: C 438 LYS cc_start: 0.7920 (mttt) cc_final: 0.7576 (mttm) REVERT: C 462 SER cc_start: 0.8349 (m) cc_final: 0.7894 (p) REVERT: C 463 ASN cc_start: 0.7897 (t0) cc_final: 0.7164 (t0) REVERT: C 465 GLU cc_start: 0.7767 (tp30) cc_final: 0.7489 (tp30) REVERT: C 466 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6868 (mm-30) REVERT: C 494 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6612 (ttp-110) REVERT: C 521 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7275 (tm-30) outliers start: 35 outliers final: 16 residues processed: 447 average time/residue: 1.4853 time to fit residues: 715.5511 Evaluate side-chains 397 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 379 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 363 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 113 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 173 HIS A 297 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13230 Z= 0.177 Angle : 0.582 11.468 17916 Z= 0.296 Chirality : 0.043 0.260 1950 Planarity : 0.004 0.042 2310 Dihedral : 5.060 33.568 2040 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.93 % Allowed : 16.70 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1563 helix: 1.35 (0.20), residues: 663 sheet: 1.16 (0.28), residues: 276 loop : 0.28 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 34 HIS 0.003 0.001 HIS A 297 PHE 0.031 0.001 PHE A 33 TYR 0.014 0.001 TYR C 118 ARG 0.002 0.000 ARG C 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 389 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7342 (tptp) REVERT: A 16 MET cc_start: 0.7465 (ttp) cc_final: 0.7014 (ptp) REVERT: A 44 MET cc_start: 0.7458 (ttt) cc_final: 0.7039 (ttt) REVERT: A 49 MET cc_start: 0.6297 (ttt) cc_final: 0.5881 (tmm) REVERT: A 61 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7584 (mtpm) REVERT: A 62 LYS cc_start: 0.6588 (ttpp) cc_final: 0.6241 (ttmm) REVERT: A 102 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.7025 (mtm-85) REVERT: A 203 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 232 LYS cc_start: 0.8431 (mttt) cc_final: 0.8117 (mttm) REVERT: A 301 SER cc_start: 0.7491 (t) cc_final: 0.6958 (p) REVERT: A 302 ASP cc_start: 0.7338 (p0) cc_final: 0.7062 (p0) REVERT: A 336 VAL cc_start: 0.7878 (p) cc_final: 0.7633 (t) REVERT: A 363 THR cc_start: 0.7652 (m) cc_final: 0.7310 (t) REVERT: A 380 LYS cc_start: 0.6620 (mtpt) cc_final: 0.6252 (mttp) REVERT: A 438 LYS cc_start: 0.8123 (mttt) cc_final: 0.7897 (mttp) REVERT: A 465 GLU cc_start: 0.7632 (tp30) cc_final: 0.7368 (tp30) REVERT: A 470 ASP cc_start: 0.7738 (m-30) cc_final: 0.7357 (m-30) REVERT: A 521 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 16 MET cc_start: 0.7339 (ttp) cc_final: 0.6900 (ptp) REVERT: B 33 PHE cc_start: 0.7386 (t80) cc_final: 0.7114 (t80) REVERT: B 44 MET cc_start: 0.7390 (ttt) cc_final: 0.6785 (ttt) REVERT: B 49 MET cc_start: 0.6441 (ttt) cc_final: 0.5735 (tmm) REVERT: B 51 GLU cc_start: 0.6611 (tp30) cc_final: 0.6382 (tp30) REVERT: B 61 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7624 (ttpp) REVERT: B 120 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7641 (ttmm) REVERT: B 121 LYS cc_start: 0.7635 (ttpp) cc_final: 0.7413 (tttm) REVERT: B 135 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 156 GLU cc_start: 0.7692 (tt0) cc_final: 0.7308 (tt0) REVERT: B 203 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 232 LYS cc_start: 0.8193 (mttt) cc_final: 0.7955 (mttm) REVERT: B 244 GLU cc_start: 0.7774 (tp30) cc_final: 0.7392 (tp30) REVERT: B 288 ARG cc_start: 0.7408 (mtp85) cc_final: 0.6976 (mtm-85) REVERT: B 303 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7565 (mtpp) REVERT: B 311 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6519 (mm-30) REVERT: B 329 GLU cc_start: 0.7418 (tt0) cc_final: 0.7101 (tt0) REVERT: B 363 THR cc_start: 0.7550 (m) cc_final: 0.7124 (t) REVERT: B 370 GLN cc_start: 0.7198 (mt0) cc_final: 0.6736 (mm110) REVERT: B 463 ASN cc_start: 0.7816 (t0) cc_final: 0.7180 (t0) REVERT: B 465 GLU cc_start: 0.7695 (tp30) cc_final: 0.7480 (tp30) REVERT: B 466 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6685 (mm-30) REVERT: B 485 LYS cc_start: 0.7465 (ttpp) cc_final: 0.7179 (ttpp) REVERT: B 492 TYR cc_start: 0.8004 (t80) cc_final: 0.7443 (t80) REVERT: B 521 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 10 PHE cc_start: 0.6290 (t80) cc_final: 0.6079 (t80) REVERT: C 16 MET cc_start: 0.7391 (ttp) cc_final: 0.6961 (ptp) REVERT: C 33 PHE cc_start: 0.7348 (t80) cc_final: 0.7005 (t80) REVERT: C 44 MET cc_start: 0.7476 (ttt) cc_final: 0.7186 (ttt) REVERT: C 61 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7207 (mtpm) REVERT: C 66 GLU cc_start: 0.7623 (pt0) cc_final: 0.6921 (pm20) REVERT: C 95 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7316 (mtt180) REVERT: C 99 GLU cc_start: 0.7451 (tt0) cc_final: 0.7218 (tt0) REVERT: C 120 LYS cc_start: 0.7733 (mttt) cc_final: 0.7504 (ttmm) REVERT: C 156 GLU cc_start: 0.7691 (tt0) cc_final: 0.7108 (pm20) REVERT: C 232 LYS cc_start: 0.8407 (mttt) cc_final: 0.8075 (mttp) REVERT: C 234 ASP cc_start: 0.8075 (m-30) cc_final: 0.7846 (p0) REVERT: C 288 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6980 (mtm-85) REVERT: C 312 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7782 (ttp-170) REVERT: C 346 ASN cc_start: 0.7697 (m-40) cc_final: 0.7419 (m-40) REVERT: C 355 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7360 (p0) REVERT: C 363 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7117 (p) REVERT: C 370 GLN cc_start: 0.7301 (mt0) cc_final: 0.6751 (mm110) REVERT: C 380 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6814 (mmtp) REVERT: C 438 LYS cc_start: 0.7920 (mttt) cc_final: 0.7564 (mttm) REVERT: C 440 ASN cc_start: 0.7453 (p0) cc_final: 0.7246 (p0) REVERT: C 462 SER cc_start: 0.8347 (m) cc_final: 0.7907 (p) REVERT: C 463 ASN cc_start: 0.7890 (t0) cc_final: 0.7127 (t0) REVERT: C 465 GLU cc_start: 0.7740 (tp30) cc_final: 0.7471 (tp30) REVERT: C 466 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6798 (mm-30) REVERT: C 492 TYR cc_start: 0.7832 (t80) cc_final: 0.7515 (t80) REVERT: C 494 ARG cc_start: 0.6856 (ttp-110) cc_final: 0.6600 (ttp-110) REVERT: C 521 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7261 (tm-30) outliers start: 27 outliers final: 9 residues processed: 404 average time/residue: 1.4846 time to fit residues: 644.5766 Evaluate side-chains 386 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 374 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 501 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.0010 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.0020 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 overall best weight: 0.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13230 Z= 0.206 Angle : 0.581 16.154 17916 Z= 0.297 Chirality : 0.043 0.262 1950 Planarity : 0.004 0.046 2310 Dihedral : 4.891 27.983 2040 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.36 % Allowed : 17.42 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.21), residues: 1563 helix: 1.50 (0.21), residues: 660 sheet: 1.09 (0.28), residues: 276 loop : 0.24 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 349 HIS 0.005 0.001 HIS B 297 PHE 0.015 0.001 PHE B 431 TYR 0.013 0.001 TYR C 326 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 378 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7724 (mmmm) cc_final: 0.7288 (tptp) REVERT: A 44 MET cc_start: 0.7434 (ttt) cc_final: 0.7042 (ttt) REVERT: A 49 MET cc_start: 0.6302 (ttt) cc_final: 0.5906 (tmm) REVERT: A 61 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7568 (mtpm) REVERT: A 102 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.7030 (mtm180) REVERT: A 203 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 232 LYS cc_start: 0.8442 (mttt) cc_final: 0.8099 (mttm) REVERT: A 288 ARG cc_start: 0.7525 (mtp85) cc_final: 0.7054 (mtm180) REVERT: A 289 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6415 (ttt90) REVERT: A 302 ASP cc_start: 0.7346 (p0) cc_final: 0.7067 (p0) REVERT: A 336 VAL cc_start: 0.7870 (p) cc_final: 0.7656 (t) REVERT: A 363 THR cc_start: 0.7708 (m) cc_final: 0.7376 (t) REVERT: A 380 LYS cc_start: 0.6522 (mtpt) cc_final: 0.6213 (mttp) REVERT: A 407 GLU cc_start: 0.7396 (tt0) cc_final: 0.7170 (tt0) REVERT: A 465 GLU cc_start: 0.7646 (tp30) cc_final: 0.7370 (tp30) REVERT: A 470 ASP cc_start: 0.7712 (m-30) cc_final: 0.7348 (m-30) REVERT: A 521 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 16 MET cc_start: 0.7391 (ttp) cc_final: 0.6891 (ptp) REVERT: B 33 PHE cc_start: 0.7401 (t80) cc_final: 0.7128 (t80) REVERT: B 44 MET cc_start: 0.7396 (ttt) cc_final: 0.6807 (ttt) REVERT: B 49 MET cc_start: 0.6505 (ttt) cc_final: 0.5826 (tmm) REVERT: B 51 GLU cc_start: 0.6625 (tp30) cc_final: 0.6391 (tp30) REVERT: B 61 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7659 (ttpp) REVERT: B 120 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7645 (ttmm) REVERT: B 121 LYS cc_start: 0.7635 (ttpp) cc_final: 0.7382 (tttm) REVERT: B 135 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7416 (mt-10) REVERT: B 156 GLU cc_start: 0.7656 (tt0) cc_final: 0.7272 (tt0) REVERT: B 203 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B 232 LYS cc_start: 0.8271 (mttt) cc_final: 0.8031 (mttm) REVERT: B 244 GLU cc_start: 0.7742 (tp30) cc_final: 0.7360 (tp30) REVERT: B 249 VAL cc_start: 0.8065 (m) cc_final: 0.7864 (m) REVERT: B 288 ARG cc_start: 0.7419 (mtp85) cc_final: 0.6990 (mtm-85) REVERT: B 293 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6190 (mm) REVERT: B 303 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7545 (mtpp) REVERT: B 311 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6517 (mm-30) REVERT: B 329 GLU cc_start: 0.7388 (tt0) cc_final: 0.7067 (tt0) REVERT: B 336 VAL cc_start: 0.7827 (p) cc_final: 0.7549 (t) REVERT: B 347 ILE cc_start: 0.7707 (tp) cc_final: 0.7485 (tp) REVERT: B 363 THR cc_start: 0.7523 (m) cc_final: 0.7093 (t) REVERT: B 366 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6402 (mt-10) REVERT: B 370 GLN cc_start: 0.7208 (mt0) cc_final: 0.6743 (mm110) REVERT: B 381 CYS cc_start: 0.5795 (m) cc_final: 0.5214 (t) REVERT: B 457 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7495 (ttpp) REVERT: B 463 ASN cc_start: 0.7810 (t0) cc_final: 0.7237 (t0) REVERT: B 465 GLU cc_start: 0.7717 (tp30) cc_final: 0.7434 (tp30) REVERT: B 466 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6850 (mm-30) REVERT: B 485 LYS cc_start: 0.7493 (ttpp) cc_final: 0.7211 (ttpp) REVERT: B 492 TYR cc_start: 0.8012 (t80) cc_final: 0.7440 (t80) REVERT: B 521 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 7 MET cc_start: 0.6911 (ttm) cc_final: 0.6711 (ttm) REVERT: C 10 PHE cc_start: 0.6332 (t80) cc_final: 0.6097 (t80) REVERT: C 16 MET cc_start: 0.7443 (ttp) cc_final: 0.7051 (ptp) REVERT: C 33 PHE cc_start: 0.7387 (t80) cc_final: 0.7036 (t80) REVERT: C 61 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7256 (ttmm) REVERT: C 66 GLU cc_start: 0.7628 (pt0) cc_final: 0.6876 (pm20) REVERT: C 95 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7364 (mtt180) REVERT: C 99 GLU cc_start: 0.7451 (tt0) cc_final: 0.7225 (tt0) REVERT: C 120 LYS cc_start: 0.7746 (mttt) cc_final: 0.7523 (ttmm) REVERT: C 156 GLU cc_start: 0.7666 (tt0) cc_final: 0.7078 (pm20) REVERT: C 203 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7066 (mm-30) REVERT: C 232 LYS cc_start: 0.8415 (mttt) cc_final: 0.8058 (mttp) REVERT: C 288 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6865 (mtm-85) REVERT: C 312 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7777 (ttp-170) REVERT: C 346 ASN cc_start: 0.7710 (m-40) cc_final: 0.7429 (m-40) REVERT: C 355 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7384 (p0) REVERT: C 363 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7145 (p) REVERT: C 370 GLN cc_start: 0.7304 (mt0) cc_final: 0.6707 (mm110) REVERT: C 380 LYS cc_start: 0.7169 (mtpt) cc_final: 0.6809 (mmtp) REVERT: C 438 LYS cc_start: 0.7918 (mttt) cc_final: 0.7601 (mttm) REVERT: C 462 SER cc_start: 0.8405 (m) cc_final: 0.7987 (p) REVERT: C 463 ASN cc_start: 0.7878 (t0) cc_final: 0.7163 (t0) REVERT: C 465 GLU cc_start: 0.7770 (tp30) cc_final: 0.7497 (tp30) REVERT: C 466 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6776 (mm-30) REVERT: C 488 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7274 (mt-10) REVERT: C 492 TYR cc_start: 0.7852 (t80) cc_final: 0.7543 (t80) REVERT: C 494 ARG cc_start: 0.6880 (ttp-110) cc_final: 0.6618 (ttp-110) REVERT: C 518 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: C 521 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7225 (tm-30) outliers start: 33 outliers final: 15 residues processed: 392 average time/residue: 1.5898 time to fit residues: 673.0530 Evaluate side-chains 389 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 368 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 297 HIS B 482 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13230 Z= 0.332 Angle : 0.607 12.750 17916 Z= 0.311 Chirality : 0.046 0.273 1950 Planarity : 0.005 0.051 2310 Dihedral : 4.882 27.301 2040 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.86 % Allowed : 17.77 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1563 helix: 1.34 (0.20), residues: 663 sheet: 1.06 (0.28), residues: 270 loop : 0.14 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 349 HIS 0.004 0.001 HIS B 260 PHE 0.019 0.002 PHE C 439 TYR 0.015 0.002 TYR A 414 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 377 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7836 (mmmm) cc_final: 0.7387 (tptp) REVERT: A 44 MET cc_start: 0.7508 (ttt) cc_final: 0.7137 (ttt) REVERT: A 49 MET cc_start: 0.6314 (ttt) cc_final: 0.5969 (tmm) REVERT: A 61 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7605 (mtpm) REVERT: A 203 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 232 LYS cc_start: 0.8515 (mttt) cc_final: 0.8223 (mttm) REVERT: A 288 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7186 (mtp180) REVERT: A 289 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6533 (ttt90) REVERT: A 302 ASP cc_start: 0.7380 (p0) cc_final: 0.7133 (p0) REVERT: A 363 THR cc_start: 0.7712 (m) cc_final: 0.7402 (t) REVERT: A 370 GLN cc_start: 0.7291 (mm110) cc_final: 0.6947 (mp10) REVERT: A 380 LYS cc_start: 0.6551 (mtpt) cc_final: 0.6239 (mttp) REVERT: A 406 ASP cc_start: 0.7546 (t0) cc_final: 0.7036 (t0) REVERT: A 407 GLU cc_start: 0.7385 (tt0) cc_final: 0.7136 (tt0) REVERT: A 465 GLU cc_start: 0.7710 (tp30) cc_final: 0.7436 (tp30) REVERT: A 470 ASP cc_start: 0.7679 (m-30) cc_final: 0.7367 (m-30) REVERT: A 521 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 33 PHE cc_start: 0.7461 (t80) cc_final: 0.7204 (t80) REVERT: B 44 MET cc_start: 0.7391 (ttt) cc_final: 0.6822 (ttt) REVERT: B 49 MET cc_start: 0.6387 (ttt) cc_final: 0.5685 (tmm) REVERT: B 51 GLU cc_start: 0.6636 (tp30) cc_final: 0.6383 (tp30) REVERT: B 61 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7655 (ttpp) REVERT: B 86 ASP cc_start: 0.7714 (t70) cc_final: 0.7435 (t0) REVERT: B 110 SER cc_start: 0.8459 (t) cc_final: 0.8088 (t) REVERT: B 120 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7660 (ttmm) REVERT: B 121 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7375 (tttm) REVERT: B 135 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7495 (mt-10) REVERT: B 156 GLU cc_start: 0.7572 (tt0) cc_final: 0.7213 (tt0) REVERT: B 203 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7330 (mm-30) REVERT: B 232 LYS cc_start: 0.8311 (mttt) cc_final: 0.8049 (mttt) REVERT: B 303 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7541 (mtpp) REVERT: B 311 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6469 (mm-30) REVERT: B 329 GLU cc_start: 0.7423 (tt0) cc_final: 0.7098 (tt0) REVERT: B 347 ILE cc_start: 0.7712 (tp) cc_final: 0.7498 (tp) REVERT: B 363 THR cc_start: 0.7577 (m) cc_final: 0.7154 (t) REVERT: B 370 GLN cc_start: 0.7267 (mt0) cc_final: 0.6786 (mm110) REVERT: B 457 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7438 (ttpp) REVERT: B 463 ASN cc_start: 0.7833 (t0) cc_final: 0.7312 (t0) REVERT: B 465 GLU cc_start: 0.7696 (tp30) cc_final: 0.7472 (tp30) REVERT: B 466 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6833 (mm-30) REVERT: B 485 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7258 (ttpp) REVERT: B 490 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: B 492 TYR cc_start: 0.8030 (t80) cc_final: 0.7125 (t80) REVERT: B 521 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 10 PHE cc_start: 0.6389 (t80) cc_final: 0.6167 (t80) REVERT: C 33 PHE cc_start: 0.7452 (t80) cc_final: 0.7110 (t80) REVERT: C 44 MET cc_start: 0.7410 (ttt) cc_final: 0.7143 (ttp) REVERT: C 61 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7352 (mtpm) REVERT: C 99 GLU cc_start: 0.7451 (tt0) cc_final: 0.7224 (tt0) REVERT: C 120 LYS cc_start: 0.7790 (mttt) cc_final: 0.7554 (ttmm) REVERT: C 141 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7865 (mm110) REVERT: C 156 GLU cc_start: 0.7645 (tt0) cc_final: 0.7061 (pm20) REVERT: C 203 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7100 (mm-30) REVERT: C 232 LYS cc_start: 0.8452 (mttt) cc_final: 0.8094 (mttp) REVERT: C 288 ARG cc_start: 0.7491 (mtp85) cc_final: 0.6854 (mtm-85) REVERT: C 312 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7773 (ttp-170) REVERT: C 346 ASN cc_start: 0.7699 (m-40) cc_final: 0.7403 (m-40) REVERT: C 355 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7443 (p0) REVERT: C 363 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7253 (p) REVERT: C 370 GLN cc_start: 0.7419 (mt0) cc_final: 0.6849 (mm110) REVERT: C 380 LYS cc_start: 0.7045 (mtpt) cc_final: 0.6799 (mmtp) REVERT: C 438 LYS cc_start: 0.7870 (mttt) cc_final: 0.7570 (mttm) REVERT: C 462 SER cc_start: 0.8409 (m) cc_final: 0.8022 (p) REVERT: C 463 ASN cc_start: 0.7865 (t0) cc_final: 0.7154 (t0) REVERT: C 465 GLU cc_start: 0.7801 (tp30) cc_final: 0.7509 (tp30) REVERT: C 466 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6769 (mm-30) REVERT: C 494 ARG cc_start: 0.6905 (ttp-110) cc_final: 0.6647 (ttp-110) REVERT: C 518 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: C 521 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7188 (tm-30) outliers start: 40 outliers final: 19 residues processed: 396 average time/residue: 1.5721 time to fit residues: 667.6890 Evaluate side-chains 397 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 371 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 440 ASN B 482 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13230 Z= 0.200 Angle : 0.558 10.067 17916 Z= 0.285 Chirality : 0.043 0.262 1950 Planarity : 0.004 0.051 2310 Dihedral : 4.715 27.066 2040 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.93 % Allowed : 17.84 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1563 helix: 1.50 (0.21), residues: 663 sheet: 1.01 (0.29), residues: 270 loop : 0.14 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.005 0.001 HIS B 297 PHE 0.016 0.001 PHE B 431 TYR 0.013 0.001 TYR A 118 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 380 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7834 (mmmm) cc_final: 0.7403 (tptp) REVERT: A 44 MET cc_start: 0.7367 (ttt) cc_final: 0.6997 (ttt) REVERT: A 49 MET cc_start: 0.6296 (ttt) cc_final: 0.5968 (tmm) REVERT: A 61 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7624 (mtpm) REVERT: A 232 LYS cc_start: 0.8469 (mttt) cc_final: 0.8143 (mttm) REVERT: A 288 ARG cc_start: 0.7448 (mtp85) cc_final: 0.6907 (mtm-85) REVERT: A 289 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6506 (ttt90) REVERT: A 302 ASP cc_start: 0.7367 (p0) cc_final: 0.7110 (p0) REVERT: A 363 THR cc_start: 0.7707 (m) cc_final: 0.7417 (t) REVERT: A 370 GLN cc_start: 0.7258 (mm110) cc_final: 0.6904 (mp10) REVERT: A 380 LYS cc_start: 0.6504 (mtpt) cc_final: 0.6215 (mttp) REVERT: A 386 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7490 (mtmt) REVERT: A 406 ASP cc_start: 0.7526 (t0) cc_final: 0.6923 (t0) REVERT: A 407 GLU cc_start: 0.7361 (tt0) cc_final: 0.7113 (tt0) REVERT: A 465 GLU cc_start: 0.7713 (tp30) cc_final: 0.7421 (tp30) REVERT: A 470 ASP cc_start: 0.7630 (m-30) cc_final: 0.7318 (m-30) REVERT: A 521 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7035 (tm-30) REVERT: B 16 MET cc_start: 0.7392 (ttp) cc_final: 0.7191 (ptm) REVERT: B 33 PHE cc_start: 0.7458 (t80) cc_final: 0.7188 (t80) REVERT: B 44 MET cc_start: 0.7365 (ttt) cc_final: 0.6775 (ttt) REVERT: B 49 MET cc_start: 0.6417 (ttt) cc_final: 0.6133 (tmm) REVERT: B 51 GLU cc_start: 0.6657 (tp30) cc_final: 0.6431 (tp30) REVERT: B 61 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7681 (ttpp) REVERT: B 86 ASP cc_start: 0.7706 (t70) cc_final: 0.7405 (t0) REVERT: B 110 SER cc_start: 0.8459 (t) cc_final: 0.8088 (t) REVERT: B 120 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7663 (ttmm) REVERT: B 121 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7370 (tttm) REVERT: B 135 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 156 GLU cc_start: 0.7555 (tt0) cc_final: 0.7187 (tt0) REVERT: B 203 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 232 LYS cc_start: 0.8323 (mttt) cc_final: 0.8065 (mttt) REVERT: B 244 GLU cc_start: 0.7784 (tp30) cc_final: 0.7388 (tp30) REVERT: B 288 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6942 (mtm-85) REVERT: B 303 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7477 (mtpp) REVERT: B 311 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6466 (mm-30) REVERT: B 326 TYR cc_start: 0.7220 (m-80) cc_final: 0.6729 (m-10) REVERT: B 329 GLU cc_start: 0.7378 (tt0) cc_final: 0.7061 (tt0) REVERT: B 347 ILE cc_start: 0.7742 (tp) cc_final: 0.7519 (tp) REVERT: B 363 THR cc_start: 0.7554 (m) cc_final: 0.7123 (t) REVERT: B 370 GLN cc_start: 0.7249 (mt0) cc_final: 0.6762 (mm110) REVERT: B 380 LYS cc_start: 0.6505 (mtpt) cc_final: 0.6138 (mmtp) REVERT: B 381 CYS cc_start: 0.5791 (m) cc_final: 0.5159 (t) REVERT: B 457 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7340 (ttpp) REVERT: B 463 ASN cc_start: 0.7827 (t0) cc_final: 0.7246 (t0) REVERT: B 465 GLU cc_start: 0.7705 (tp30) cc_final: 0.7474 (tp30) REVERT: B 466 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 475 ASN cc_start: 0.8220 (m-40) cc_final: 0.8000 (m-40) REVERT: B 485 LYS cc_start: 0.7519 (ttpp) cc_final: 0.7234 (ttpp) REVERT: B 492 TYR cc_start: 0.8022 (t80) cc_final: 0.7417 (t80) REVERT: B 494 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6743 (ttm-80) REVERT: B 521 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 10 PHE cc_start: 0.6379 (t80) cc_final: 0.6097 (t80) REVERT: C 16 MET cc_start: 0.7501 (ttp) cc_final: 0.7087 (ptp) REVERT: C 33 PHE cc_start: 0.7411 (t80) cc_final: 0.7055 (t80) REVERT: C 44 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7217 (ttp) REVERT: C 61 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7475 (ttmm) REVERT: C 99 GLU cc_start: 0.7452 (tt0) cc_final: 0.7225 (tt0) REVERT: C 120 LYS cc_start: 0.7790 (mttt) cc_final: 0.7556 (ttmm) REVERT: C 141 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7861 (mm110) REVERT: C 203 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7141 (mm-30) REVERT: C 232 LYS cc_start: 0.8419 (mttt) cc_final: 0.8046 (mttp) REVERT: C 244 GLU cc_start: 0.7758 (tp30) cc_final: 0.7473 (tp30) REVERT: C 288 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6861 (mtm-85) REVERT: C 312 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7770 (ttp-170) REVERT: C 346 ASN cc_start: 0.7691 (m-40) cc_final: 0.7394 (m-40) REVERT: C 355 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7499 (p0) REVERT: C 363 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7243 (p) REVERT: C 370 GLN cc_start: 0.7347 (mt0) cc_final: 0.6730 (mm110) REVERT: C 380 LYS cc_start: 0.7058 (mtpt) cc_final: 0.6810 (mmtp) REVERT: C 438 LYS cc_start: 0.7888 (mttt) cc_final: 0.7535 (mttm) REVERT: C 462 SER cc_start: 0.8406 (m) cc_final: 0.8041 (p) REVERT: C 463 ASN cc_start: 0.7862 (t0) cc_final: 0.7114 (t0) REVERT: C 465 GLU cc_start: 0.7788 (tp30) cc_final: 0.7488 (tp30) REVERT: C 466 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6772 (mm-30) REVERT: C 480 ASP cc_start: 0.7204 (m-30) cc_final: 0.6857 (m-30) REVERT: C 494 ARG cc_start: 0.6888 (ttp-110) cc_final: 0.6627 (ttp-110) REVERT: C 518 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: C 521 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7108 (tm-30) outliers start: 41 outliers final: 18 residues processed: 401 average time/residue: 1.5414 time to fit residues: 663.6495 Evaluate side-chains 397 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 371 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 440 ASN B 504 GLN C 13 GLN C 376 HIS C 440 ASN C 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13230 Z= 0.290 Angle : 0.614 19.844 17916 Z= 0.313 Chirality : 0.045 0.263 1950 Planarity : 0.005 0.057 2310 Dihedral : 4.702 27.281 2040 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.21 % Allowed : 18.70 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1563 helix: 1.36 (0.20), residues: 663 sheet: 1.04 (0.28), residues: 270 loop : 0.07 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.005 0.001 HIS A 376 PHE 0.019 0.002 PHE B 431 TYR 0.014 0.001 TYR C 326 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 378 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7393 (tptp) REVERT: A 44 MET cc_start: 0.7390 (ttt) cc_final: 0.7017 (ttt) REVERT: A 49 MET cc_start: 0.6325 (ttt) cc_final: 0.5974 (tmm) REVERT: A 61 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7599 (mtpm) REVERT: A 203 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 232 LYS cc_start: 0.8506 (mttt) cc_final: 0.8176 (mttm) REVERT: A 288 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7079 (mtp180) REVERT: A 289 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6576 (ttt90) REVERT: A 302 ASP cc_start: 0.7370 (p0) cc_final: 0.7109 (p0) REVERT: A 363 THR cc_start: 0.7673 (m) cc_final: 0.7374 (t) REVERT: A 370 GLN cc_start: 0.7272 (mm110) cc_final: 0.6925 (mp10) REVERT: A 406 ASP cc_start: 0.7531 (t0) cc_final: 0.6998 (t0) REVERT: A 465 GLU cc_start: 0.7707 (tp30) cc_final: 0.7423 (tp30) REVERT: A 470 ASP cc_start: 0.7666 (m-30) cc_final: 0.7274 (m-30) REVERT: A 521 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 16 MET cc_start: 0.7427 (ttp) cc_final: 0.6866 (ptp) REVERT: B 21 LYS cc_start: 0.7299 (tppp) cc_final: 0.7015 (tttt) REVERT: B 33 PHE cc_start: 0.7490 (t80) cc_final: 0.7233 (t80) REVERT: B 44 MET cc_start: 0.7380 (ttt) cc_final: 0.6880 (ttt) REVERT: B 51 GLU cc_start: 0.6678 (tp30) cc_final: 0.6436 (tp30) REVERT: B 61 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7704 (ttpp) REVERT: B 86 ASP cc_start: 0.7689 (t70) cc_final: 0.7380 (t0) REVERT: B 120 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7666 (ttmm) REVERT: B 121 LYS cc_start: 0.7624 (ttpp) cc_final: 0.7367 (tttm) REVERT: B 135 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 156 GLU cc_start: 0.7541 (tt0) cc_final: 0.7176 (tt0) REVERT: B 203 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 232 LYS cc_start: 0.8329 (mttt) cc_final: 0.8077 (mttt) REVERT: B 288 ARG cc_start: 0.7462 (mtp85) cc_final: 0.6938 (mtm-85) REVERT: B 297 HIS cc_start: 0.7472 (m90) cc_final: 0.7260 (m-70) REVERT: B 303 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7509 (mtpp) REVERT: B 311 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6464 (mm-30) REVERT: B 326 TYR cc_start: 0.7260 (m-80) cc_final: 0.6634 (m-10) REVERT: B 329 GLU cc_start: 0.7374 (tt0) cc_final: 0.7067 (tt0) REVERT: B 347 ILE cc_start: 0.7767 (tp) cc_final: 0.7566 (tp) REVERT: B 363 THR cc_start: 0.7589 (m) cc_final: 0.7150 (t) REVERT: B 380 LYS cc_start: 0.6554 (mtpt) cc_final: 0.6200 (mmtp) REVERT: B 463 ASN cc_start: 0.7815 (t0) cc_final: 0.7294 (t0) REVERT: B 465 GLU cc_start: 0.7714 (tp30) cc_final: 0.7464 (tp30) REVERT: B 466 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6843 (mm-30) REVERT: B 475 ASN cc_start: 0.8227 (m-40) cc_final: 0.8018 (m-40) REVERT: B 485 LYS cc_start: 0.7522 (ttpp) cc_final: 0.7253 (ttpp) REVERT: B 492 TYR cc_start: 0.8046 (t80) cc_final: 0.7391 (t80) REVERT: B 494 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6823 (ttm-80) REVERT: B 521 GLU cc_start: 0.7641 (tm-30) cc_final: 0.6995 (tm-30) REVERT: C 10 PHE cc_start: 0.6440 (t80) cc_final: 0.6149 (t80) REVERT: C 16 MET cc_start: 0.7526 (ttp) cc_final: 0.7101 (ptp) REVERT: C 33 PHE cc_start: 0.7444 (t80) cc_final: 0.7110 (t80) REVERT: C 44 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7155 (ttp) REVERT: C 61 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7495 (mtpm) REVERT: C 99 GLU cc_start: 0.7443 (tt0) cc_final: 0.7223 (tt0) REVERT: C 110 SER cc_start: 0.8072 (t) cc_final: 0.7528 (p) REVERT: C 120 LYS cc_start: 0.7779 (mttt) cc_final: 0.7539 (ttmm) REVERT: C 141 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7864 (mm110) REVERT: C 203 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 232 LYS cc_start: 0.8425 (mttt) cc_final: 0.8045 (mttp) REVERT: C 288 ARG cc_start: 0.7450 (mtp85) cc_final: 0.6862 (mtm-85) REVERT: C 312 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7784 (ttp-170) REVERT: C 346 ASN cc_start: 0.7700 (m-40) cc_final: 0.7399 (m-40) REVERT: C 355 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7442 (p0) REVERT: C 363 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7256 (p) REVERT: C 370 GLN cc_start: 0.7387 (mt0) cc_final: 0.6780 (mm110) REVERT: C 380 LYS cc_start: 0.6940 (mtpt) cc_final: 0.6723 (mmtp) REVERT: C 438 LYS cc_start: 0.7910 (mttt) cc_final: 0.7565 (mttm) REVERT: C 462 SER cc_start: 0.8389 (m) cc_final: 0.7993 (p) REVERT: C 463 ASN cc_start: 0.7825 (t0) cc_final: 0.7087 (t0) REVERT: C 465 GLU cc_start: 0.7807 (tp30) cc_final: 0.7496 (tp30) REVERT: C 466 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6741 (mm-30) REVERT: C 480 ASP cc_start: 0.7217 (m-30) cc_final: 0.6875 (m-30) REVERT: C 494 ARG cc_start: 0.6902 (ttp-110) cc_final: 0.6628 (ttp-110) REVERT: C 521 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7204 (tm-30) outliers start: 45 outliers final: 23 residues processed: 397 average time/residue: 1.5309 time to fit residues: 650.9273 Evaluate side-chains 405 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 376 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN C 440 ASN C 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13230 Z= 0.212 Angle : 0.590 15.552 17916 Z= 0.299 Chirality : 0.043 0.258 1950 Planarity : 0.004 0.057 2310 Dihedral : 4.686 34.497 2040 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.21 % Allowed : 19.27 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1563 helix: 1.44 (0.21), residues: 663 sheet: 1.01 (0.29), residues: 270 loop : 0.08 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 349 HIS 0.004 0.001 HIS B 376 PHE 0.015 0.001 PHE B 188 TYR 0.013 0.001 TYR A 118 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 377 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7404 (tptp) REVERT: A 44 MET cc_start: 0.7352 (ttt) cc_final: 0.6954 (ttt) REVERT: A 49 MET cc_start: 0.6299 (ttt) cc_final: 0.5808 (tmm) REVERT: A 61 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7511 (mtpm) REVERT: A 154 ASP cc_start: 0.7451 (t0) cc_final: 0.7118 (t0) REVERT: A 232 LYS cc_start: 0.8518 (mttt) cc_final: 0.8193 (mttm) REVERT: A 288 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6917 (mtm-85) REVERT: A 289 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6534 (ttt90) REVERT: A 302 ASP cc_start: 0.7240 (p0) cc_final: 0.7009 (p0) REVERT: A 363 THR cc_start: 0.7661 (m) cc_final: 0.7361 (t) REVERT: A 406 ASP cc_start: 0.7433 (t0) cc_final: 0.6899 (t0) REVERT: A 465 GLU cc_start: 0.7715 (tp30) cc_final: 0.7430 (tp30) REVERT: A 470 ASP cc_start: 0.7644 (m-30) cc_final: 0.7232 (m-30) REVERT: A 521 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 16 MET cc_start: 0.7396 (ttp) cc_final: 0.6928 (ptp) REVERT: B 33 PHE cc_start: 0.7495 (t80) cc_final: 0.7248 (t80) REVERT: B 44 MET cc_start: 0.7344 (ttt) cc_final: 0.6831 (ttt) REVERT: B 51 GLU cc_start: 0.6661 (tp30) cc_final: 0.6458 (tp30) REVERT: B 61 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7679 (ttpp) REVERT: B 110 SER cc_start: 0.8475 (t) cc_final: 0.8115 (t) REVERT: B 120 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7690 (ttmm) REVERT: B 121 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7313 (tttm) REVERT: B 135 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 156 GLU cc_start: 0.7529 (tt0) cc_final: 0.7165 (tt0) REVERT: B 203 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 232 LYS cc_start: 0.8330 (mttt) cc_final: 0.8092 (mttt) REVERT: B 244 GLU cc_start: 0.7766 (tp30) cc_final: 0.7380 (tp30) REVERT: B 288 ARG cc_start: 0.7438 (mtp85) cc_final: 0.6939 (mtm-85) REVERT: B 297 HIS cc_start: 0.7544 (m90) cc_final: 0.7335 (m-70) REVERT: B 303 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7479 (mtpp) REVERT: B 311 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6454 (mm-30) REVERT: B 326 TYR cc_start: 0.7206 (m-80) cc_final: 0.6558 (m-10) REVERT: B 329 GLU cc_start: 0.7400 (tt0) cc_final: 0.7097 (tt0) REVERT: B 347 ILE cc_start: 0.7702 (tp) cc_final: 0.7491 (tp) REVERT: B 363 THR cc_start: 0.7551 (m) cc_final: 0.7102 (t) REVERT: B 366 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6375 (mt-10) REVERT: B 370 GLN cc_start: 0.7249 (mt0) cc_final: 0.6819 (mm110) REVERT: B 380 LYS cc_start: 0.6334 (mtpt) cc_final: 0.6019 (mmtp) REVERT: B 381 CYS cc_start: 0.5836 (m) cc_final: 0.5067 (t) REVERT: B 441 GLU cc_start: 0.7805 (mp0) cc_final: 0.7503 (mp0) REVERT: B 463 ASN cc_start: 0.7814 (t0) cc_final: 0.7233 (t0) REVERT: B 465 GLU cc_start: 0.7709 (tp30) cc_final: 0.7459 (tp30) REVERT: B 466 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6846 (mm-30) REVERT: B 485 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7253 (ttpp) REVERT: B 492 TYR cc_start: 0.8024 (t80) cc_final: 0.7278 (t80) REVERT: B 494 ARG cc_start: 0.7007 (ttm-80) cc_final: 0.6768 (ttm-80) REVERT: B 521 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7024 (tm-30) REVERT: C 10 PHE cc_start: 0.6444 (t80) cc_final: 0.6148 (t80) REVERT: C 16 MET cc_start: 0.7512 (ttp) cc_final: 0.7134 (ptp) REVERT: C 33 PHE cc_start: 0.7442 (t80) cc_final: 0.7111 (t80) REVERT: C 44 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7218 (ttp) REVERT: C 61 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7414 (mtpm) REVERT: C 99 GLU cc_start: 0.7448 (tt0) cc_final: 0.7230 (tt0) REVERT: C 110 SER cc_start: 0.8074 (t) cc_final: 0.7570 (p) REVERT: C 120 LYS cc_start: 0.7781 (mttt) cc_final: 0.7554 (ttmm) REVERT: C 141 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7862 (mm110) REVERT: C 156 GLU cc_start: 0.7637 (tt0) cc_final: 0.6919 (pm20) REVERT: C 203 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7189 (mm-30) REVERT: C 232 LYS cc_start: 0.8495 (mttt) cc_final: 0.8121 (mttp) REVERT: C 288 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6859 (mtm-85) REVERT: C 346 ASN cc_start: 0.7692 (m-40) cc_final: 0.7391 (m-40) REVERT: C 355 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7539 (p0) REVERT: C 363 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7236 (p) REVERT: C 370 GLN cc_start: 0.7359 (mt0) cc_final: 0.6763 (mm110) REVERT: C 438 LYS cc_start: 0.7897 (mttt) cc_final: 0.7533 (mttm) REVERT: C 463 ASN cc_start: 0.7753 (t0) cc_final: 0.7024 (t0) REVERT: C 465 GLU cc_start: 0.7822 (tp30) cc_final: 0.7508 (tp30) REVERT: C 466 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6722 (mm-30) REVERT: C 480 ASP cc_start: 0.7179 (m-30) cc_final: 0.6845 (m-30) REVERT: C 494 ARG cc_start: 0.6883 (ttp-110) cc_final: 0.6612 (ttp-110) REVERT: C 521 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7173 (tm-30) outliers start: 31 outliers final: 22 residues processed: 391 average time/residue: 1.5358 time to fit residues: 644.9278 Evaluate side-chains 401 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 374 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS C 440 ASN C 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 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 : 0.003 0.057 13230 Z= 0.222 Angle : 0.605 12.990 17916 Z= 0.302 Chirality : 0.043 0.258 1950 Planarity : 0.005 0.058 2310 Dihedral : 4.613 32.292 2040 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.93 % Allowed : 20.20 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1563 helix: 1.59 (0.21), residues: 645 sheet: 0.92 (0.31), residues: 261 loop : -0.05 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 349 HIS 0.004 0.001 HIS A 376 PHE 0.019 0.001 PHE A 33 TYR 0.013 0.001 TYR A 118 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 368 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7906 (mmmm) cc_final: 0.7460 (tptp) REVERT: A 44 MET cc_start: 0.7349 (ttt) cc_final: 0.6955 (ttt) REVERT: A 49 MET cc_start: 0.6296 (ttt) cc_final: 0.5806 (tmm) REVERT: A 61 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7503 (mtpm) REVERT: A 203 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 232 LYS cc_start: 0.8464 (mttt) cc_final: 0.8147 (mttm) REVERT: A 288 ARG cc_start: 0.7439 (mtp85) cc_final: 0.6895 (mtm-85) REVERT: A 289 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6560 (ttt90) REVERT: A 302 ASP cc_start: 0.7200 (p0) cc_final: 0.6941 (p0) REVERT: A 363 THR cc_start: 0.7655 (m) cc_final: 0.7371 (t) REVERT: A 370 GLN cc_start: 0.7259 (mm110) cc_final: 0.6881 (mp10) REVERT: A 406 ASP cc_start: 0.7448 (t0) cc_final: 0.6917 (t0) REVERT: A 407 GLU cc_start: 0.7383 (tt0) cc_final: 0.7136 (tt0) REVERT: A 465 GLU cc_start: 0.7700 (tp30) cc_final: 0.7429 (tp30) REVERT: A 521 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 16 MET cc_start: 0.7377 (ttp) cc_final: 0.7048 (ptm) REVERT: B 33 PHE cc_start: 0.7418 (t80) cc_final: 0.7183 (t80) REVERT: B 44 MET cc_start: 0.7357 (ttt) cc_final: 0.6846 (ttt) REVERT: B 51 GLU cc_start: 0.6704 (tp30) cc_final: 0.6496 (tp30) REVERT: B 61 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7670 (ttpp) REVERT: B 110 SER cc_start: 0.8476 (t) cc_final: 0.8116 (t) REVERT: B 120 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7690 (ttmm) REVERT: B 121 LYS cc_start: 0.7594 (ttpp) cc_final: 0.7299 (tttm) REVERT: B 135 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 156 GLU cc_start: 0.7518 (tt0) cc_final: 0.7168 (tt0) REVERT: B 203 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 232 LYS cc_start: 0.8341 (mttt) cc_final: 0.8072 (mttm) REVERT: B 244 GLU cc_start: 0.7768 (tp30) cc_final: 0.7405 (tp30) REVERT: B 288 ARG cc_start: 0.7445 (mtp85) cc_final: 0.6937 (mtm-85) REVERT: B 303 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7464 (mtpp) REVERT: B 311 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6447 (mm-30) REVERT: B 312 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7755 (ttp-170) REVERT: B 326 TYR cc_start: 0.7206 (m-80) cc_final: 0.6716 (m-10) REVERT: B 329 GLU cc_start: 0.7410 (tt0) cc_final: 0.7116 (tt0) REVERT: B 347 ILE cc_start: 0.7678 (tp) cc_final: 0.7463 (tp) REVERT: B 370 GLN cc_start: 0.7251 (mt0) cc_final: 0.6825 (mm110) REVERT: B 380 LYS cc_start: 0.6370 (mtpt) cc_final: 0.6044 (mmtp) REVERT: B 381 CYS cc_start: 0.5533 (m) cc_final: 0.4889 (t) REVERT: B 463 ASN cc_start: 0.7816 (t0) cc_final: 0.7251 (t0) REVERT: B 465 GLU cc_start: 0.7708 (tp30) cc_final: 0.7457 (tp30) REVERT: B 466 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 485 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7253 (ttpp) REVERT: B 492 TYR cc_start: 0.8038 (t80) cc_final: 0.7280 (t80) REVERT: B 494 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6835 (ttm-80) REVERT: B 521 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 10 PHE cc_start: 0.6407 (t80) cc_final: 0.6103 (t80) REVERT: C 16 MET cc_start: 0.7494 (ttp) cc_final: 0.7086 (ptp) REVERT: C 33 PHE cc_start: 0.7451 (t80) cc_final: 0.7089 (t80) REVERT: C 44 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7179 (ttp) REVERT: C 51 GLU cc_start: 0.7009 (tp30) cc_final: 0.6743 (tm-30) REVERT: C 61 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7360 (mtpm) REVERT: C 62 LYS cc_start: 0.6659 (ttpp) cc_final: 0.6064 (ttpp) REVERT: C 99 GLU cc_start: 0.7461 (tt0) cc_final: 0.7229 (tt0) REVERT: C 110 SER cc_start: 0.8090 (t) cc_final: 0.7591 (p) REVERT: C 120 LYS cc_start: 0.7787 (mttt) cc_final: 0.7523 (ttmm) REVERT: C 141 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7856 (mm110) REVERT: C 142 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: C 156 GLU cc_start: 0.7634 (tt0) cc_final: 0.6919 (pm20) REVERT: C 203 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7213 (mm-30) REVERT: C 232 LYS cc_start: 0.8491 (mttt) cc_final: 0.8122 (mttp) REVERT: C 288 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6859 (mtm-85) REVERT: C 346 ASN cc_start: 0.7692 (m-40) cc_final: 0.7387 (m-40) REVERT: C 355 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7542 (p0) REVERT: C 363 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7226 (p) REVERT: C 366 GLU cc_start: 0.6685 (pm20) cc_final: 0.6282 (pp20) REVERT: C 370 GLN cc_start: 0.7347 (mt0) cc_final: 0.6751 (mm110) REVERT: C 438 LYS cc_start: 0.7896 (mttt) cc_final: 0.7535 (mttm) REVERT: C 463 ASN cc_start: 0.7780 (t0) cc_final: 0.7050 (t0) REVERT: C 465 GLU cc_start: 0.7827 (tp30) cc_final: 0.7512 (tp30) REVERT: C 466 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6702 (mm-30) REVERT: C 480 ASP cc_start: 0.7173 (m-30) cc_final: 0.6841 (m-30) REVERT: C 494 ARG cc_start: 0.6885 (ttp-110) cc_final: 0.6615 (ttp-110) REVERT: C 521 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7186 (tm-30) outliers start: 27 outliers final: 20 residues processed: 380 average time/residue: 1.4945 time to fit residues: 610.1069 Evaluate side-chains 391 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 365 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 440 ASN C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13230 Z= 0.200 Angle : 0.598 11.929 17916 Z= 0.300 Chirality : 0.043 0.256 1950 Planarity : 0.004 0.054 2310 Dihedral : 4.551 31.152 2040 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.93 % Allowed : 20.27 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1563 helix: 1.69 (0.21), residues: 645 sheet: 0.93 (0.30), residues: 267 loop : -0.01 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 419 HIS 0.003 0.001 HIS C 376 PHE 0.014 0.001 PHE B 188 TYR 0.014 0.001 TYR A 118 ARG 0.004 0.000 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 362 time to evaluate : 1.480 Fit side-chains REVERT: A 9 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7444 (tptp) REVERT: A 44 MET cc_start: 0.7341 (ttt) cc_final: 0.6936 (ttt) REVERT: A 49 MET cc_start: 0.6288 (ttt) cc_final: 0.5801 (tmm) REVERT: A 61 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7568 (mtpm) REVERT: A 203 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 232 LYS cc_start: 0.8449 (mttt) cc_final: 0.8136 (mttm) REVERT: A 288 ARG cc_start: 0.7437 (mtp85) cc_final: 0.6893 (mtm-85) REVERT: A 289 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6551 (ttt90) REVERT: A 302 ASP cc_start: 0.7163 (p0) cc_final: 0.6932 (p0) REVERT: A 363 THR cc_start: 0.7645 (m) cc_final: 0.7375 (t) REVERT: A 407 GLU cc_start: 0.7367 (tt0) cc_final: 0.7137 (tt0) REVERT: A 465 GLU cc_start: 0.7710 (tp30) cc_final: 0.7423 (tp30) REVERT: A 521 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 16 MET cc_start: 0.7410 (ttp) cc_final: 0.6979 (ptp) REVERT: B 33 PHE cc_start: 0.7485 (t80) cc_final: 0.7212 (t80) REVERT: B 44 MET cc_start: 0.7354 (ttt) cc_final: 0.6839 (ttt) REVERT: B 51 GLU cc_start: 0.6689 (tp30) cc_final: 0.6482 (tp30) REVERT: B 61 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7655 (ttpp) REVERT: B 110 SER cc_start: 0.8482 (t) cc_final: 0.8125 (t) REVERT: B 120 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7682 (ttmm) REVERT: B 121 LYS cc_start: 0.7583 (ttpp) cc_final: 0.7283 (tttm) REVERT: B 135 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 156 GLU cc_start: 0.7518 (tt0) cc_final: 0.7155 (tt0) REVERT: B 232 LYS cc_start: 0.8313 (mttt) cc_final: 0.8058 (mttm) REVERT: B 244 GLU cc_start: 0.7762 (tp30) cc_final: 0.7413 (tp30) REVERT: B 288 ARG cc_start: 0.7438 (mtp85) cc_final: 0.6943 (mtm-85) REVERT: B 303 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7473 (mtpp) REVERT: B 308 ASP cc_start: 0.7730 (m-30) cc_final: 0.7343 (p0) REVERT: B 311 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6409 (mm-30) REVERT: B 312 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7745 (ttp-170) REVERT: B 326 TYR cc_start: 0.7181 (m-80) cc_final: 0.6693 (m-10) REVERT: B 329 GLU cc_start: 0.7393 (tt0) cc_final: 0.7124 (tt0) REVERT: B 347 ILE cc_start: 0.7648 (tp) cc_final: 0.7437 (tp) REVERT: B 370 GLN cc_start: 0.7246 (mt0) cc_final: 0.6808 (mm110) REVERT: B 380 LYS cc_start: 0.6314 (mtpt) cc_final: 0.6017 (mmtp) REVERT: B 463 ASN cc_start: 0.7807 (t0) cc_final: 0.7194 (t0) REVERT: B 465 GLU cc_start: 0.7702 (tp30) cc_final: 0.7446 (tp30) REVERT: B 466 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6833 (mm-30) REVERT: B 485 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7252 (ttpp) REVERT: B 492 TYR cc_start: 0.7994 (t80) cc_final: 0.7345 (t80) REVERT: B 494 ARG cc_start: 0.6991 (ttm-80) cc_final: 0.6771 (ttm-80) REVERT: B 521 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7019 (tm-30) REVERT: C 10 PHE cc_start: 0.6382 (t80) cc_final: 0.6096 (t80) REVERT: C 16 MET cc_start: 0.7399 (ttp) cc_final: 0.7022 (ptp) REVERT: C 33 PHE cc_start: 0.7497 (t80) cc_final: 0.7146 (t80) REVERT: C 44 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7122 (ttp) REVERT: C 51 GLU cc_start: 0.7017 (tp30) cc_final: 0.6756 (tm-30) REVERT: C 61 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7218 (mtpm) REVERT: C 62 LYS cc_start: 0.6653 (ttpp) cc_final: 0.6077 (ttpp) REVERT: C 99 GLU cc_start: 0.7457 (tt0) cc_final: 0.7225 (tt0) REVERT: C 110 SER cc_start: 0.8104 (t) cc_final: 0.7609 (p) REVERT: C 120 LYS cc_start: 0.7787 (mttt) cc_final: 0.7526 (ttmm) REVERT: C 141 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7788 (mm110) REVERT: C 142 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: C 156 GLU cc_start: 0.7632 (tt0) cc_final: 0.7020 (pm20) REVERT: C 178 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7231 (mtm-85) REVERT: C 203 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 232 LYS cc_start: 0.8452 (mttt) cc_final: 0.8087 (mttp) REVERT: C 288 ARG cc_start: 0.7433 (mtp85) cc_final: 0.6862 (mtm-85) REVERT: C 346 ASN cc_start: 0.7686 (m-40) cc_final: 0.7380 (m-40) REVERT: C 363 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7204 (p) REVERT: C 370 GLN cc_start: 0.7319 (mt0) cc_final: 0.6735 (mm110) REVERT: C 381 CYS cc_start: 0.5659 (m) cc_final: 0.5100 (t) REVERT: C 438 LYS cc_start: 0.7864 (mttt) cc_final: 0.7506 (mttm) REVERT: C 463 ASN cc_start: 0.7771 (t0) cc_final: 0.6997 (t0) REVERT: C 465 GLU cc_start: 0.7824 (tp30) cc_final: 0.7504 (tp30) REVERT: C 466 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6690 (mm-30) REVERT: C 480 ASP cc_start: 0.7143 (m-30) cc_final: 0.6820 (m-30) REVERT: C 494 ARG cc_start: 0.6872 (ttp-110) cc_final: 0.6597 (ttp-110) REVERT: C 495 ASN cc_start: 0.7013 (t0) cc_final: 0.6582 (t0) REVERT: C 521 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7108 (tm-30) outliers start: 27 outliers final: 20 residues processed: 375 average time/residue: 1.5352 time to fit residues: 617.0083 Evaluate side-chains 385 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 360 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 440 ASN C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109881 restraints weight = 17457.582| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.94 r_work: 0.3279 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13230 Z= 0.220 Angle : 0.614 11.217 17916 Z= 0.305 Chirality : 0.044 0.290 1950 Planarity : 0.005 0.048 2310 Dihedral : 4.540 30.562 2040 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 20.27 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1563 helix: 1.66 (0.21), residues: 645 sheet: 0.96 (0.30), residues: 267 loop : -0.02 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 349 HIS 0.003 0.001 HIS A 376 PHE 0.019 0.001 PHE A 33 TYR 0.014 0.001 TYR A 118 ARG 0.011 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8559.13 seconds wall clock time: 152 minutes 46.49 seconds (9166.49 seconds total)