Starting phenix.real_space_refine on Fri Jun 13 14:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ct6_26983/06_2025/8ct6_26983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ct6_26983/06_2025/8ct6_26983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ct6_26983/06_2025/8ct6_26983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ct6_26983/06_2025/8ct6_26983.map" model { file = "/net/cci-nas-00/data/ceres_data/8ct6_26983/06_2025/8ct6_26983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ct6_26983/06_2025/8ct6_26983.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 73 5.16 5 C 9357 2.51 5 N 2516 2.21 5 O 2972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14918 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3778 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Chain: "A" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3726 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 Chain: "C" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3643 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 3 Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Conformer: "B" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} bond proxies already assigned to first conformer: 913 Chain: "K" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 905 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.69, per 1000 atoms: 0.65 Number of scatterers: 14918 At special positions: 0 Unit cell: (124.355, 119.13, 151.525, 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 73 16.00 O 2972 8.00 N 2516 7.00 C 9357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 464 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 464 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 601 " - " ASN A 269 " " NAG A 602 " - " ASN A 127 " " NAG A 603 " - " ASN A 287 " " NAG B 601 " - " ASN B 287 " " NAG B 602 " - " ASN B 11 " " NAG B 603 " - " ASN B 23 " " NAG B 604 " - " ASN B 269 " " NAG C 601 " - " ASN C 23 " " NAG C 602 " - " ASN C 287 " " NAG C 603 " - " ASN C 127 " " NAG D 1 " - " ASN B 87 " " NAG E 1 " - " ASN B 127 " " NAG F 1 " - " ASN A 87 " " NAG G 1 " - " ASN C 87 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 46 sheets defined 21.8% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 68 through 73 removed outlier: 3.856A pdb=" N SER B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 removed outlier: 3.947A pdb=" N SER B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 4.455A pdb=" N TRP B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 364 through 386 removed outlier: 3.604A pdb=" N MET B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 453 removed outlier: 3.915A pdb=" N LEU B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.926A pdb=" N GLU A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 removed outlier: 3.916A pdb=" N SER A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.660A pdb=" N TRP A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 401 through 453 removed outlier: 4.005A pdb=" N LYS A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.544A pdb=" N LEU C 71 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 removed outlier: 3.753A pdb=" N SER C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 123 removed outlier: 4.270A pdb=" N TRP C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'C' and resid 368 through 386 removed outlier: 3.556A pdb=" N ASN C 380 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 451 removed outlier: 3.949A pdb=" N VAL C 442 " --> pdb=" O HIS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 485 through 490 removed outlier: 4.332A pdb=" N TYR C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 490' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.829A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.866A pdb=" N ALA K 83 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.939A pdb=" N SER J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.888A pdb=" N VAL B 30 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.362A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 79 " --> pdb=" O ILE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.599A pdb=" N SER B 110 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 7.892A pdb=" N LEU B 176 " --> pdb=" O PRO B 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 138 removed outlier: 7.209A pdb=" N ALA B 135 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LYS B 141 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 166 Processing sheet with id=AB2, first strand: chain 'B' and resid 457 through 461 removed outlier: 4.761A pdb=" N GLU B 459 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU B 466 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.938A pdb=" N GLY A 350 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AB6, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AB7, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.234A pdb=" N LEU A 41 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N CYS A 275 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.280A pdb=" N ILE A 79 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 108 through 115 removed outlier: 6.414A pdb=" N TYR A 253 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 108 through 115 removed outlier: 6.414A pdb=" N TYR A 253 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 133 through 138 removed outlier: 4.786A pdb=" N CYS A 136 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 143 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AC4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AC5, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AC6, first strand: chain 'C' and resid 7 through 8 removed outlier: 7.104A pdb=" N TYR C 7 " --> pdb=" O TRP C 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AC8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.849A pdb=" N VAL C 30 " --> pdb=" O MET C 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.332A pdb=" N ILE C 79 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.522A pdb=" N SER C 110 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 253 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU C 176 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 172 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU C 176 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 113 through 115 removed outlier: 6.472A pdb=" N TYR C 253 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU C 176 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 172 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AD5, first strand: chain 'C' and resid 133 through 137 Processing sheet with id=AD6, first strand: chain 'C' and resid 161 through 166 Processing sheet with id=AD7, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.814A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.612A pdb=" N MET L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 30 through 30A Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.737A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.737A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.583A pdb=" N MET K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR K 49 " --> pdb=" O MET K 33 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 30 through 30A Processing sheet with id=AE8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.523A pdb=" N GLU J 10 " --> pdb=" O SER J 108 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.523A pdb=" N GLU J 10 " --> pdb=" O SER J 108 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1539 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: 5.14 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4794 1.34 - 1.46: 3751 1.46 - 1.58: 6614 1.58 - 1.71: 0 1.71 - 1.83: 102 Bond restraints: 15261 Sorted by residual: bond pdb=" N VAL L 78 " pdb=" CA VAL L 78 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.23e+00 bond pdb=" N GLU L 79 " pdb=" CA GLU L 79 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.83e+00 bond pdb=" N ASP K 94 " pdb=" CA ASP K 94 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.04e-02 9.25e+03 7.64e+00 bond pdb=" N GLY C 347 " pdb=" CA GLY C 347 " ideal model delta sigma weight residual 1.447 1.477 -0.030 1.08e-02 8.57e+03 7.61e+00 bond pdb=" N ILE C 345 " pdb=" CA ILE C 345 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.37e-02 5.33e+03 6.54e+00 ... (remaining 15256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 20060 1.63 - 3.25: 517 3.25 - 4.88: 72 4.88 - 6.51: 30 6.51 - 8.13: 4 Bond angle restraints: 20683 Sorted by residual: angle pdb=" C GLY C 343 " pdb=" N MET C 344 " pdb=" CA MET C 344 " ideal model delta sigma weight residual 122.77 116.51 6.26 1.33e+00 5.65e-01 2.22e+01 angle pdb=" N ILE C 345 " pdb=" CA ILE C 345 " pdb=" C ILE C 345 " ideal model delta sigma weight residual 112.83 108.72 4.11 9.90e-01 1.02e+00 1.72e+01 angle pdb=" C ALA C 139 " pdb=" CA ALA C 139 " pdb=" CB ALA C 139 " ideal model delta sigma weight residual 115.89 110.94 4.95 1.32e+00 5.74e-01 1.41e+01 angle pdb=" C LEU A 290 " pdb=" N PRO A 291 " pdb=" CA PRO A 291 " ideal model delta sigma weight residual 119.05 122.74 -3.69 1.11e+00 8.12e-01 1.10e+01 angle pdb=" CA GLY C 343 " pdb=" C GLY C 343 " pdb=" O GLY C 343 " ideal model delta sigma weight residual 120.75 117.39 3.36 1.03e+00 9.43e-01 1.06e+01 ... (remaining 20678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 8408 21.98 - 43.97: 795 43.97 - 65.95: 122 65.95 - 87.93: 42 87.93 - 109.92: 15 Dihedral angle restraints: 9382 sinusoidal: 4029 harmonic: 5353 Sorted by residual: dihedral pdb=" CB CYS A 471 " pdb=" SG CYS A 471 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual -86.00 1.79 -87.79 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual -86.00 -2.38 -83.62 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 42 " pdb=" SG CYS B 42 " pdb=" SG CYS B 275 " pdb=" CB CYS B 275 " ideal model delta sinusoidal sigma weight residual -86.00 -26.39 -59.61 1 1.00e+01 1.00e-02 4.74e+01 ... (remaining 9379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2036 0.071 - 0.143: 229 0.143 - 0.214: 9 0.214 - 0.286: 6 0.286 - 0.357: 2 Chirality restraints: 2282 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 23 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 287 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2279 not shown) Planarity restraints: 2657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 23 " -0.029 2.00e-02 2.50e+03 2.57e-02 8.28e+00 pdb=" CG ASN C 23 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 23 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 23 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 39 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO K 40 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 40 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 40 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 58 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO L 59 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.027 5.00e-02 4.00e+02 ... (remaining 2654 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3014 2.77 - 3.30: 14376 3.30 - 3.84: 25964 3.84 - 4.37: 30818 4.37 - 4.90: 52697 Nonbonded interactions: 126869 Sorted by model distance: nonbonded pdb=" OD1 ASN B 127 " pdb=" OG1 THR B 129 " model vdw 2.240 3.040 nonbonded pdb=" O GLU A 213 " pdb=" NH2 ARG A 217 " model vdw 2.246 3.120 nonbonded pdb=" NH1 ARG L 61 " pdb=" OD2 ASP L 82 " model vdw 2.247 3.120 nonbonded pdb=" O LEU B 416 " pdb=" OG1 THR B 420 " model vdw 2.250 3.040 nonbonded pdb=" ND2 ASN B 31 " pdb=" O LEU B 33 " model vdw 2.263 3.120 ... (remaining 126864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 451 or resid 459 through 490 or resid 601 throug \ h 603)) selection = (chain 'B' and (resid 4 through 321 or resid 338 through 354 or resid 361 throug \ h 451 or resid 459 through 490 or resid 602 through 604)) selection = (chain 'C' and (resid 4 through 321 or resid 338 through 354 or resid 361 throug \ h 490 or resid 601 through 603)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 1 through 55 or resid 57 through 111)) selection = (chain 'J' and (resid 1 through 55 or resid 57 through 111)) } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.37 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.430 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 0.041 15306 Z= 0.225 Angle : 0.661 8.283 20796 Z= 0.346 Chirality : 0.046 0.357 2282 Planarity : 0.004 0.060 2643 Dihedral : 17.172 109.918 5902 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.00 % Allowed : 23.20 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.03 (0.19), residues: 1832 helix: 1.88 (0.28), residues: 321 sheet: 0.10 (0.26), residues: 433 loop : -0.57 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 103 HIS 0.006 0.001 HIS C 126 PHE 0.031 0.001 PHE A 111 TYR 0.011 0.001 TYR C 7 ARG 0.004 0.000 ARG B 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 14) link_NAG-ASN : angle 3.32452 ( 42) link_BETA1-4 : bond 0.00564 ( 7) link_BETA1-4 : angle 1.67935 ( 21) link_ALPHA1-3 : bond 0.00069 ( 2) link_ALPHA1-3 : angle 2.01546 ( 6) hydrogen bonds : bond 0.20176 ( 546) hydrogen bonds : angle 8.23233 ( 1539) SS BOND : bond 0.00366 ( 22) SS BOND : angle 1.37815 ( 44) covalent geometry : bond 0.00450 (15261) covalent geometry : angle 0.63928 (20683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7336 (m-40) REVERT: L 75 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7919 (mm) REVERT: L 85 THR cc_start: 0.8019 (m) cc_final: 0.7257 (p) REVERT: K 42 GLN cc_start: 0.8025 (mp10) cc_final: 0.7593 (mp10) REVERT: J 5 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7625 (tp40) REVERT: J 19 LYS cc_start: 0.8919 (mmtm) cc_final: 0.8564 (mmmm) REVERT: J 59 TYR cc_start: 0.7488 (m-80) cc_final: 0.7086 (m-80) outliers start: 16 outliers final: 7 residues processed: 199 average time/residue: 0.3265 time to fit residues: 92.2029 Evaluate side-chains 181 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 0.0980 chunk 47 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083343 restraints weight = 38671.179| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.22 r_work: 0.3055 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15306 Z= 0.161 Angle : 0.585 7.762 20796 Z= 0.299 Chirality : 0.044 0.315 2282 Planarity : 0.004 0.047 2643 Dihedral : 9.391 69.119 2492 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 3.30 % Allowed : 22.51 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.21 (0.19), residues: 1832 helix: 1.99 (0.27), residues: 325 sheet: 0.22 (0.26), residues: 428 loop : -0.45 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 36 HIS 0.011 0.001 HIS C 438 PHE 0.026 0.001 PHE A 111 TYR 0.012 0.001 TYR A 446 ARG 0.003 0.000 ARG K 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 14) link_NAG-ASN : angle 2.47875 ( 42) link_BETA1-4 : bond 0.00400 ( 7) link_BETA1-4 : angle 2.06316 ( 21) link_ALPHA1-3 : bond 0.00554 ( 2) link_ALPHA1-3 : angle 2.30761 ( 6) hydrogen bonds : bond 0.04342 ( 546) hydrogen bonds : angle 5.84947 ( 1539) SS BOND : bond 0.00315 ( 22) SS BOND : angle 0.90570 ( 44) covalent geometry : bond 0.00361 (15261) covalent geometry : angle 0.56890 (20683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 MET cc_start: 0.7735 (mmp) cc_final: 0.7422 (mmp) REVERT: C 40 LYS cc_start: 0.7764 (mtpt) cc_final: 0.7456 (ttmm) REVERT: C 429 LEU cc_start: 0.8120 (mt) cc_final: 0.7917 (mm) REVERT: C 437 PHE cc_start: 0.8360 (t80) cc_final: 0.8079 (t80) REVERT: L 75 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (mm) REVERT: L 85 THR cc_start: 0.7348 (m) cc_final: 0.6708 (p) REVERT: K 24 LYS cc_start: 0.8345 (mptt) cc_final: 0.8027 (ttpp) REVERT: K 42 GLN cc_start: 0.8139 (mp10) cc_final: 0.7568 (mp10) REVERT: K 53 LYS cc_start: 0.8127 (mptt) cc_final: 0.7696 (mtmt) REVERT: K 74 ASN cc_start: 0.8296 (p0) cc_final: 0.7373 (m-40) REVERT: J 59 TYR cc_start: 0.7156 (m-80) cc_final: 0.6573 (m-80) outliers start: 53 outliers final: 30 residues processed: 230 average time/residue: 0.2966 time to fit residues: 99.5923 Evaluate side-chains 208 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 87 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN J 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.121590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081646 restraints weight = 39111.416| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.17 r_work: 0.3024 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15306 Z= 0.232 Angle : 0.601 6.482 20796 Z= 0.308 Chirality : 0.045 0.257 2282 Planarity : 0.004 0.036 2643 Dihedral : 8.032 59.470 2485 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 4.10 % Allowed : 22.01 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.13 (0.19), residues: 1832 helix: 1.92 (0.28), residues: 324 sheet: 0.20 (0.26), residues: 430 loop : -0.52 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 103 HIS 0.005 0.001 HIS C 126 PHE 0.031 0.002 PHE A 111 TYR 0.014 0.001 TYR B 349 ARG 0.005 0.001 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 14) link_NAG-ASN : angle 2.16902 ( 42) link_BETA1-4 : bond 0.00472 ( 7) link_BETA1-4 : angle 1.98307 ( 21) link_ALPHA1-3 : bond 0.00637 ( 2) link_ALPHA1-3 : angle 2.00039 ( 6) hydrogen bonds : bond 0.04135 ( 546) hydrogen bonds : angle 5.62386 ( 1539) SS BOND : bond 0.00408 ( 22) SS BOND : angle 0.94780 ( 44) covalent geometry : bond 0.00535 (15261) covalent geometry : angle 0.58831 (20683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.8149 (tt0) cc_final: 0.7813 (pt0) REVERT: C 429 LEU cc_start: 0.8149 (mt) cc_final: 0.7925 (mm) REVERT: L 75 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7789 (mm) REVERT: L 85 THR cc_start: 0.7618 (m) cc_final: 0.6907 (p) REVERT: K 24 LYS cc_start: 0.8463 (mptt) cc_final: 0.8028 (mptt) REVERT: K 42 GLN cc_start: 0.8062 (mp10) cc_final: 0.7481 (mp-120) REVERT: K 53 LYS cc_start: 0.8137 (mptt) cc_final: 0.7756 (mmmm) REVERT: K 61 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6716 (ptp-110) REVERT: K 74 ASN cc_start: 0.8337 (p0) cc_final: 0.7448 (m-40) REVERT: J 59 TYR cc_start: 0.7223 (m-80) cc_final: 0.6660 (m-80) outliers start: 66 outliers final: 50 residues processed: 229 average time/residue: 0.2916 time to fit residues: 96.1758 Evaluate side-chains 230 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 128 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082852 restraints weight = 42892.428| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.35 r_work: 0.3055 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15306 Z= 0.127 Angle : 0.545 9.070 20796 Z= 0.277 Chirality : 0.043 0.235 2282 Planarity : 0.003 0.032 2643 Dihedral : 6.758 55.772 2485 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 3.98 % Allowed : 22.26 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.24 (0.19), residues: 1832 helix: 2.05 (0.27), residues: 326 sheet: 0.23 (0.25), residues: 433 loop : -0.45 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 103 HIS 0.004 0.001 HIS B 353 PHE 0.029 0.001 PHE B 437 TYR 0.013 0.001 TYR B 349 ARG 0.002 0.000 ARG C 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 14) link_NAG-ASN : angle 2.08478 ( 42) link_BETA1-4 : bond 0.00456 ( 7) link_BETA1-4 : angle 1.91559 ( 21) link_ALPHA1-3 : bond 0.00940 ( 2) link_ALPHA1-3 : angle 2.02534 ( 6) hydrogen bonds : bond 0.03534 ( 546) hydrogen bonds : angle 5.27292 ( 1539) SS BOND : bond 0.00269 ( 22) SS BOND : angle 0.79712 ( 44) covalent geometry : bond 0.00283 (15261) covalent geometry : angle 0.53246 (20683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 HIS cc_start: 0.7343 (t70) cc_final: 0.7004 (t70) REVERT: A 384 GLU cc_start: 0.8190 (tt0) cc_final: 0.7838 (pt0) REVERT: C 47 ILE cc_start: 0.8507 (mm) cc_final: 0.8306 (tp) REVERT: L 75 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7862 (mm) REVERT: L 85 THR cc_start: 0.7525 (m) cc_final: 0.6824 (p) REVERT: K 11 LEU cc_start: 0.8844 (tp) cc_final: 0.8519 (tp) REVERT: K 34 SER cc_start: 0.8991 (m) cc_final: 0.8748 (m) REVERT: K 42 GLN cc_start: 0.8158 (mp10) cc_final: 0.7603 (mp-120) REVERT: K 53 LYS cc_start: 0.8252 (mptt) cc_final: 0.7810 (mmmm) REVERT: K 61 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6712 (ptp-110) REVERT: K 74 ASN cc_start: 0.8275 (p0) cc_final: 0.7330 (m-40) REVERT: J 59 TYR cc_start: 0.7066 (m-80) cc_final: 0.6532 (m-80) outliers start: 64 outliers final: 51 residues processed: 245 average time/residue: 0.2976 time to fit residues: 105.3598 Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 129 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 355 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083259 restraints weight = 37986.202| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.14 r_work: 0.3066 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15306 Z= 0.132 Angle : 0.538 7.085 20796 Z= 0.274 Chirality : 0.043 0.234 2282 Planarity : 0.003 0.072 2643 Dihedral : 6.140 55.862 2485 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 4.10 % Allowed : 22.57 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.25 (0.19), residues: 1832 helix: 2.08 (0.27), residues: 327 sheet: 0.18 (0.25), residues: 445 loop : -0.42 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 103 HIS 0.011 0.001 HIS C 273 PHE 0.022 0.001 PHE B 111 TYR 0.017 0.001 TYR K 49 ARG 0.002 0.000 ARG C 433 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 14) link_NAG-ASN : angle 2.04903 ( 42) link_BETA1-4 : bond 0.00433 ( 7) link_BETA1-4 : angle 1.83364 ( 21) link_ALPHA1-3 : bond 0.00879 ( 2) link_ALPHA1-3 : angle 1.88596 ( 6) hydrogen bonds : bond 0.03406 ( 546) hydrogen bonds : angle 5.13634 ( 1539) SS BOND : bond 0.00274 ( 22) SS BOND : angle 1.05620 ( 44) covalent geometry : bond 0.00299 (15261) covalent geometry : angle 0.52476 (20683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 HIS cc_start: 0.7361 (t70) cc_final: 0.7067 (t70) REVERT: B 386 MET cc_start: 0.6846 (ppp) cc_final: 0.6622 (ppp) REVERT: A 384 GLU cc_start: 0.8134 (tt0) cc_final: 0.7786 (pt0) REVERT: C 344 MET cc_start: 0.5326 (tmm) cc_final: 0.5044 (tmm) REVERT: C 378 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6655 (ttpt) REVERT: C 437 PHE cc_start: 0.8383 (t80) cc_final: 0.8083 (t80) REVERT: C 438 HIS cc_start: 0.8418 (m90) cc_final: 0.7758 (m90) REVERT: L 75 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7920 (mm) REVERT: L 85 THR cc_start: 0.7505 (m) cc_final: 0.6804 (p) REVERT: K 11 LEU cc_start: 0.8855 (tp) cc_final: 0.8602 (tp) REVERT: K 24 LYS cc_start: 0.8371 (mptt) cc_final: 0.7985 (ttpp) REVERT: K 34 SER cc_start: 0.8983 (m) cc_final: 0.8762 (m) REVERT: K 42 GLN cc_start: 0.8151 (mp10) cc_final: 0.7598 (mp10) REVERT: K 53 LYS cc_start: 0.8282 (mptt) cc_final: 0.7840 (mmmm) REVERT: K 61 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6725 (ptp-110) REVERT: K 74 ASN cc_start: 0.8268 (p0) cc_final: 0.7360 (m-40) REVERT: J 59 TYR cc_start: 0.7136 (m-80) cc_final: 0.6633 (m-80) outliers start: 66 outliers final: 54 residues processed: 234 average time/residue: 0.3316 time to fit residues: 113.9026 Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.123053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083359 restraints weight = 36664.165| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.09 r_work: 0.3069 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15306 Z= 0.136 Angle : 0.537 7.211 20796 Z= 0.274 Chirality : 0.042 0.238 2282 Planarity : 0.003 0.058 2643 Dihedral : 5.953 55.613 2485 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 4.17 % Allowed : 23.32 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.27 (0.19), residues: 1832 helix: 2.08 (0.27), residues: 327 sheet: 0.21 (0.25), residues: 445 loop : -0.41 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 103 HIS 0.004 0.001 HIS B 353 PHE 0.022 0.001 PHE B 111 TYR 0.015 0.001 TYR K 49 ARG 0.003 0.000 ARG J 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 14) link_NAG-ASN : angle 2.02726 ( 42) link_BETA1-4 : bond 0.00443 ( 7) link_BETA1-4 : angle 1.75310 ( 21) link_ALPHA1-3 : bond 0.00826 ( 2) link_ALPHA1-3 : angle 1.74819 ( 6) hydrogen bonds : bond 0.03322 ( 546) hydrogen bonds : angle 5.06358 ( 1539) SS BOND : bond 0.00298 ( 22) SS BOND : angle 0.96512 ( 44) covalent geometry : bond 0.00310 (15261) covalent geometry : angle 0.52524 (20683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.6634 (t70) REVERT: B 314 MET cc_start: 0.7415 (mmp) cc_final: 0.6801 (tpp) REVERT: A 384 GLU cc_start: 0.8037 (tt0) cc_final: 0.7725 (pt0) REVERT: C 40 LYS cc_start: 0.7317 (tttm) cc_final: 0.7060 (tttm) REVERT: C 344 MET cc_start: 0.5324 (tmm) cc_final: 0.5034 (tmm) REVERT: C 438 HIS cc_start: 0.8412 (m90) cc_final: 0.7769 (m90) REVERT: L 75 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7911 (mm) REVERT: L 85 THR cc_start: 0.7493 (m) cc_final: 0.6800 (p) REVERT: K 11 LEU cc_start: 0.8846 (tp) cc_final: 0.8596 (tp) REVERT: K 34 SER cc_start: 0.8973 (m) cc_final: 0.8737 (m) REVERT: K 42 GLN cc_start: 0.8147 (mp10) cc_final: 0.7592 (mp10) REVERT: K 53 LYS cc_start: 0.8240 (mptt) cc_final: 0.7797 (mmmm) REVERT: K 61 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6771 (ptp-110) REVERT: K 74 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7319 (m-40) REVERT: J 3 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7776 (tm-30) REVERT: J 5 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8038 (tp40) REVERT: J 23 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8717 (ttpp) REVERT: J 59 TYR cc_start: 0.7132 (m-80) cc_final: 0.6664 (m-80) outliers start: 67 outliers final: 59 residues processed: 230 average time/residue: 0.2881 time to fit residues: 95.7054 Evaluate side-chains 247 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081193 restraints weight = 40787.010| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.27 r_work: 0.3005 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15306 Z= 0.284 Angle : 0.625 10.745 20796 Z= 0.318 Chirality : 0.045 0.247 2282 Planarity : 0.004 0.052 2643 Dihedral : 6.251 56.559 2485 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 4.73 % Allowed : 22.89 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.08 (0.19), residues: 1832 helix: 1.89 (0.27), residues: 325 sheet: 0.04 (0.25), residues: 439 loop : -0.49 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 60 HIS 0.006 0.001 HIS C 126 PHE 0.034 0.002 PHE A 111 TYR 0.016 0.002 TYR A 446 ARG 0.004 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 14) link_NAG-ASN : angle 2.17556 ( 42) link_BETA1-4 : bond 0.00460 ( 7) link_BETA1-4 : angle 1.80037 ( 21) link_ALPHA1-3 : bond 0.00602 ( 2) link_ALPHA1-3 : angle 1.77072 ( 6) hydrogen bonds : bond 0.03807 ( 546) hydrogen bonds : angle 5.33612 ( 1539) SS BOND : bond 0.00485 ( 22) SS BOND : angle 1.04268 ( 44) covalent geometry : bond 0.00658 (15261) covalent geometry : angle 0.61363 (20683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 184 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.6691 (t70) REVERT: B 361 TYR cc_start: 0.3984 (OUTLIER) cc_final: 0.1310 (t80) REVERT: A 86 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: A 384 GLU cc_start: 0.8054 (tt0) cc_final: 0.7737 (pt0) REVERT: C 344 MET cc_start: 0.5189 (tmm) cc_final: 0.4883 (tmm) REVERT: L 75 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8097 (mm) REVERT: L 85 THR cc_start: 0.7597 (m) cc_final: 0.6906 (p) REVERT: H 38 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6912 (pttt) REVERT: H 59 TYR cc_start: 0.7332 (m-80) cc_final: 0.7063 (m-80) REVERT: H 69 PHE cc_start: 0.7406 (m-80) cc_final: 0.6502 (m-80) REVERT: K 24 LYS cc_start: 0.8432 (mptt) cc_final: 0.8097 (mptt) REVERT: K 42 GLN cc_start: 0.8021 (mp10) cc_final: 0.7433 (mp10) REVERT: K 53 LYS cc_start: 0.8219 (mptt) cc_final: 0.7763 (mmmm) REVERT: K 61 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6886 (ptp-110) REVERT: K 74 ASN cc_start: 0.8277 (p0) cc_final: 0.7254 (m-40) REVERT: J 3 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7410 (tm-30) REVERT: J 5 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8121 (tp40) REVERT: J 59 TYR cc_start: 0.7277 (m-80) cc_final: 0.6688 (m-80) outliers start: 76 outliers final: 61 residues processed: 239 average time/residue: 0.2840 time to fit residues: 98.2218 Evaluate side-chains 245 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 178 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.0870 chunk 95 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.120888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081353 restraints weight = 35510.461| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.06 r_work: 0.3003 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15306 Z= 0.247 Angle : 0.607 8.090 20796 Z= 0.309 Chirality : 0.044 0.248 2282 Planarity : 0.004 0.049 2643 Dihedral : 6.257 57.760 2485 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 4.54 % Allowed : 23.07 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.00 (0.19), residues: 1832 helix: 1.77 (0.27), residues: 327 sheet: 0.02 (0.26), residues: 434 loop : -0.55 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 103 HIS 0.005 0.001 HIS C 126 PHE 0.029 0.002 PHE B 111 TYR 0.015 0.002 TYR K 49 ARG 0.003 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 14) link_NAG-ASN : angle 2.21599 ( 42) link_BETA1-4 : bond 0.00444 ( 7) link_BETA1-4 : angle 1.75652 ( 21) link_ALPHA1-3 : bond 0.00673 ( 2) link_ALPHA1-3 : angle 1.72215 ( 6) hydrogen bonds : bond 0.03677 ( 546) hydrogen bonds : angle 5.31366 ( 1539) SS BOND : bond 0.00439 ( 22) SS BOND : angle 0.96481 ( 44) covalent geometry : bond 0.00571 (15261) covalent geometry : angle 0.59498 (20683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 181 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.6646 (t70) REVERT: B 361 TYR cc_start: 0.4003 (OUTLIER) cc_final: 0.1360 (t80) REVERT: B 386 MET cc_start: 0.6945 (ppp) cc_final: 0.6676 (ppp) REVERT: A 86 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: A 384 GLU cc_start: 0.8077 (tt0) cc_final: 0.7755 (pt0) REVERT: C 344 MET cc_start: 0.5189 (tmm) cc_final: 0.4887 (tmm) REVERT: C 437 PHE cc_start: 0.8287 (t80) cc_final: 0.7987 (t80) REVERT: L 75 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8100 (mm) REVERT: L 85 THR cc_start: 0.7579 (m) cc_final: 0.6899 (p) REVERT: H 38 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6924 (pttt) REVERT: H 59 TYR cc_start: 0.7262 (m-80) cc_final: 0.7056 (m-80) REVERT: H 69 PHE cc_start: 0.7495 (m-80) cc_final: 0.6621 (m-80) REVERT: K 24 LYS cc_start: 0.8470 (mptt) cc_final: 0.8177 (mptt) REVERT: K 42 GLN cc_start: 0.7993 (mp10) cc_final: 0.7417 (mp10) REVERT: K 53 LYS cc_start: 0.8240 (mptt) cc_final: 0.7794 (mmmm) REVERT: J 3 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7406 (tm-30) REVERT: J 59 TYR cc_start: 0.7403 (m-80) cc_final: 0.6833 (m-80) outliers start: 73 outliers final: 60 residues processed: 233 average time/residue: 0.2791 time to fit residues: 94.9851 Evaluate side-chains 245 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 78 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.122819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081881 restraints weight = 43595.779| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.35 r_work: 0.3050 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15306 Z= 0.121 Angle : 0.562 9.435 20796 Z= 0.288 Chirality : 0.043 0.233 2282 Planarity : 0.003 0.045 2643 Dihedral : 5.902 57.213 2485 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 3.36 % Allowed : 24.25 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.18 (0.19), residues: 1832 helix: 1.99 (0.27), residues: 326 sheet: 0.15 (0.26), residues: 434 loop : -0.46 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.003 0.001 HIS B 353 PHE 0.031 0.001 PHE B 437 TYR 0.013 0.001 TYR K 49 ARG 0.003 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 14) link_NAG-ASN : angle 2.08840 ( 42) link_BETA1-4 : bond 0.00444 ( 7) link_BETA1-4 : angle 1.66091 ( 21) link_ALPHA1-3 : bond 0.00736 ( 2) link_ALPHA1-3 : angle 1.57560 ( 6) hydrogen bonds : bond 0.03229 ( 546) hydrogen bonds : angle 5.05768 ( 1539) SS BOND : bond 0.00252 ( 22) SS BOND : angle 0.84473 ( 44) covalent geometry : bond 0.00272 (15261) covalent geometry : angle 0.55126 (20683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.6657 (t70) REVERT: B 21 GLU cc_start: 0.6617 (pm20) cc_final: 0.5740 (pm20) REVERT: B 361 TYR cc_start: 0.4033 (OUTLIER) cc_final: 0.1579 (t80) REVERT: B 386 MET cc_start: 0.6861 (ppp) cc_final: 0.6450 (ppp) REVERT: A 384 GLU cc_start: 0.8055 (tt0) cc_final: 0.7714 (pt0) REVERT: C 344 MET cc_start: 0.5117 (tmm) cc_final: 0.4835 (tmm) REVERT: C 438 HIS cc_start: 0.8349 (m90) cc_final: 0.7746 (m90) REVERT: L 75 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7876 (mm) REVERT: L 85 THR cc_start: 0.7558 (m) cc_final: 0.6852 (p) REVERT: K 42 GLN cc_start: 0.8060 (mp10) cc_final: 0.7525 (mp10) REVERT: K 53 LYS cc_start: 0.8237 (mptt) cc_final: 0.7757 (mmmm) REVERT: K 74 ASN cc_start: 0.8325 (p0) cc_final: 0.7358 (m-40) REVERT: J 3 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7453 (tm-30) REVERT: J 19 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8593 (mmmm) REVERT: J 59 TYR cc_start: 0.7312 (m-80) cc_final: 0.6789 (m-80) outliers start: 54 outliers final: 47 residues processed: 230 average time/residue: 0.2944 time to fit residues: 97.8850 Evaluate side-chains 236 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 438 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.122498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082496 restraints weight = 39641.465| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.32 r_work: 0.3024 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15306 Z= 0.186 Angle : 0.591 8.696 20796 Z= 0.302 Chirality : 0.043 0.236 2282 Planarity : 0.004 0.042 2643 Dihedral : 5.848 57.247 2485 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 3.61 % Allowed : 24.13 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.15 (0.19), residues: 1832 helix: 1.96 (0.27), residues: 326 sheet: 0.13 (0.26), residues: 422 loop : -0.47 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.003 0.001 HIS C 126 PHE 0.054 0.002 PHE B 437 TYR 0.013 0.001 TYR B 349 ARG 0.003 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 14) link_NAG-ASN : angle 2.08679 ( 42) link_BETA1-4 : bond 0.00440 ( 7) link_BETA1-4 : angle 1.65842 ( 21) link_ALPHA1-3 : bond 0.00615 ( 2) link_ALPHA1-3 : angle 1.53775 ( 6) hydrogen bonds : bond 0.03390 ( 546) hydrogen bonds : angle 5.12644 ( 1539) SS BOND : bond 0.00372 ( 22) SS BOND : angle 1.16217 ( 44) covalent geometry : bond 0.00431 (15261) covalent geometry : angle 0.58002 (20683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.6621 (t70) REVERT: B 21 GLU cc_start: 0.6551 (pm20) cc_final: 0.5729 (pm20) REVERT: B 361 TYR cc_start: 0.4032 (OUTLIER) cc_final: 0.1463 (t80) REVERT: B 386 MET cc_start: 0.6846 (ppp) cc_final: 0.6445 (ppp) REVERT: B 438 HIS cc_start: 0.7210 (m-70) cc_final: 0.7005 (m90) REVERT: B 460 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5573 (mm) REVERT: A 384 GLU cc_start: 0.8072 (tt0) cc_final: 0.7738 (pt0) REVERT: C 344 MET cc_start: 0.5139 (tmm) cc_final: 0.4818 (tmm) REVERT: C 437 PHE cc_start: 0.8319 (t80) cc_final: 0.8047 (t80) REVERT: C 438 HIS cc_start: 0.8384 (m90) cc_final: 0.7799 (m90) REVERT: L 75 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7979 (mm) REVERT: L 85 THR cc_start: 0.7494 (m) cc_final: 0.6823 (p) REVERT: K 42 GLN cc_start: 0.8002 (mp10) cc_final: 0.7456 (mp10) REVERT: K 53 LYS cc_start: 0.8264 (mptt) cc_final: 0.7785 (mmmm) REVERT: K 61 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6960 (ptp-110) REVERT: K 74 ASN cc_start: 0.8336 (p0) cc_final: 0.7365 (m-40) REVERT: J 1 GLN cc_start: 0.7001 (pp30) cc_final: 0.6715 (pp30) REVERT: J 19 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8555 (mmmm) REVERT: J 59 TYR cc_start: 0.7341 (m-80) cc_final: 0.6788 (m-80) outliers start: 58 outliers final: 53 residues processed: 227 average time/residue: 0.2943 time to fit residues: 96.8920 Evaluate side-chains 243 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 19 optimal weight: 0.5980 chunk 174 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.082607 restraints weight = 38186.530| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.30 r_work: 0.3034 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15306 Z= 0.151 Angle : 0.581 8.760 20796 Z= 0.297 Chirality : 0.043 0.234 2282 Planarity : 0.003 0.040 2643 Dihedral : 5.648 56.460 2485 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 3.79 % Allowed : 24.13 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.17 (0.19), residues: 1832 helix: 1.97 (0.27), residues: 326 sheet: 0.12 (0.26), residues: 422 loop : -0.45 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.014 0.001 HIS B 438 PHE 0.049 0.001 PHE B 437 TYR 0.013 0.001 TYR K 49 ARG 0.003 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 14) link_NAG-ASN : angle 2.05384 ( 42) link_BETA1-4 : bond 0.00435 ( 7) link_BETA1-4 : angle 1.64261 ( 21) link_ALPHA1-3 : bond 0.00630 ( 2) link_ALPHA1-3 : angle 1.51440 ( 6) hydrogen bonds : bond 0.03282 ( 546) hydrogen bonds : angle 5.07570 ( 1539) SS BOND : bond 0.00309 ( 22) SS BOND : angle 1.09314 ( 44) covalent geometry : bond 0.00347 (15261) covalent geometry : angle 0.57017 (20683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9897.26 seconds wall clock time: 170 minutes 7.24 seconds (10207.24 seconds total)