Starting phenix.real_space_refine on Fri Jul 3 16:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ct6_26983/07_2026/8ct6_26983.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 3.23, per 1000 atoms: 0.22 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: 1.12 Conformation dependent library (CDL) restraints added in 703.7 milliseconds 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: 0.48 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: 3.00 Time building geometry restraints manager: 1.52 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 - 17.90: 7735 17.90 - 35.81: 896 35.81 - 53.71: 221 53.71 - 71.61: 36 71.61 - 89.51: 21 Dihedral angle restraints: 8909 sinusoidal: 3556 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 8906 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 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.450 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 16.193 89.515 5429 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG B 308 TYR 0.011 0.001 TYR C 7 PHE 0.031 0.001 PHE A 111 TRP 0.013 0.001 TRP H 103 HIS 0.006 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.23 (15261) covalent geometry : angle 0.63928 / 0.34 (20683) SS BOND : bond 0.00366 / 0.27 ( 22) SS BOND : angle 1.37815 / 0.99 ( 44) hydrogen bonds : bond 0.20176 / 13.34 ( 546) hydrogen bonds : angle 8.23233 / 5.74 ( 1539) link_ALPHA1-3 : bond 0.00069 / 0.04 ( 2) link_ALPHA1-3 : angle 2.01546 / 1.02 ( 6) link_BETA1-4 : bond 0.00564 / 0.29 ( 7) link_BETA1-4 : angle 1.67935 / 1.33 ( 21) link_NAG-ASN : bond 0.00700 / 0.32 ( 14) link_NAG-ASN : angle 3.32452 / 2.19 ( 42) *********************** 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 : 0.676 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: 0.7918 (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: 0.8563 (mmmm) REVERT: J 59 TYR cc_start: 0.7488 (m-80) cc_final: 0.7089 (m-80) outliers start: 16 outliers final: 7 residues processed: 199 average time/residue: 0.1314 time to fit residues: 37.5159 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 : 0.399 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.3910 r_free = 0.3910 target = 0.122950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081927 restraints weight = 49491.707| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.59 r_work: 0.3027 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15306 Z= 0.171 Angle : 0.581 7.901 20796 Z= 0.300 Chirality : 0.043 0.310 2282 Planarity : 0.004 0.048 2643 Dihedral : 5.211 56.459 2019 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 3.36 % Allowed : 22.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1832 helix: 1.97 (0.27), residues: 325 sheet: 0.22 (0.26), residues: 438 loop : -0.49 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 40 TYR 0.012 0.001 TYR A 446 PHE 0.026 0.001 PHE A 111 TRP 0.023 0.001 TRP H 36 HIS 0.010 0.001 HIS C 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15261) covalent geometry : angle 0.56806 / 0.30 (20683) SS BOND : bond 0.00332 / 0.25 ( 22) SS BOND : angle 0.90981 / 0.66 ( 44) hydrogen bonds : bond 0.04557 / 3.08 ( 546) hydrogen bonds : angle 5.92725 / 4.14 ( 1539) link_ALPHA1-3 : bond 0.00182 / 0.09 ( 2) link_ALPHA1-3 : angle 1.67542 / 0.85 ( 6) link_BETA1-4 : bond 0.00449 / 0.23 ( 7) link_BETA1-4 : angle 1.57036 / 1.19 ( 21) link_NAG-ASN : bond 0.00548 / 0.31 ( 14) link_NAG-ASN : angle 2.43996 / 1.41 ( 42) *********************** 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 248 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 MET cc_start: 0.7741 (mmp) cc_final: 0.7432 (mmp) REVERT: C 40 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7443 (ttmm) REVERT: C 429 LEU cc_start: 0.8155 (mt) cc_final: 0.7948 (mm) REVERT: C 437 PHE cc_start: 0.8367 (t80) cc_final: 0.8090 (t80) REVERT: L 61 ARG cc_start: 0.6829 (ptt90) cc_final: 0.6599 (ptt90) REVERT: L 75 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7575 (mm) REVERT: L 85 THR cc_start: 0.7398 (m) cc_final: 0.6779 (p) REVERT: K 24 LYS cc_start: 0.8334 (mptt) cc_final: 0.8022 (ttpp) REVERT: K 42 GLN cc_start: 0.8138 (mp10) cc_final: 0.7564 (mp10) REVERT: K 74 ASN cc_start: 0.8333 (p0) cc_final: 0.7429 (m-40) REVERT: K 105 GLU cc_start: 0.6983 (pp20) cc_final: 0.6767 (pp20) REVERT: J 59 TYR cc_start: 0.7141 (m-80) cc_final: 0.6564 (m-80) outliers start: 54 outliers final: 30 residues processed: 226 average time/residue: 0.1138 time to fit residues: 38.0571 Evaluate side-chains 203 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 108 VAL Chi-restraints excluded: chain C residue 111 PHE 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 H residue 77 THR 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 41 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082650 restraints weight = 48776.463| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.59 r_work: 0.3040 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15306 Z= 0.134 Angle : 0.544 6.279 20796 Z= 0.280 Chirality : 0.042 0.249 2282 Planarity : 0.003 0.031 2643 Dihedral : 4.824 56.605 2012 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 3.67 % Allowed : 22.20 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1832 helix: 2.04 (0.28), residues: 326 sheet: 0.29 (0.26), residues: 428 loop : -0.45 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.013 0.001 TYR B 349 PHE 0.023 0.001 PHE A 111 TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (15261) covalent geometry : angle 0.53261 / 0.28 (20683) SS BOND : bond 0.00269 / 0.20 ( 22) SS BOND : angle 0.86434 / 0.62 ( 44) hydrogen bonds : bond 0.03791 / 2.60 ( 546) hydrogen bonds : angle 5.45088 / 3.82 ( 1539) link_ALPHA1-3 : bond 0.00258 / 0.13 ( 2) link_ALPHA1-3 : angle 1.50274 / 0.76 ( 6) link_BETA1-4 : bond 0.00465 / 0.22 ( 7) link_BETA1-4 : angle 1.54537 / 1.19 ( 21) link_NAG-ASN : bond 0.00469 / 0.25 ( 14) link_NAG-ASN : angle 2.17425 / 1.24 ( 42) *********************** 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 253 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 HIS cc_start: 0.7415 (t70) cc_final: 0.7120 (t70) REVERT: B 437 PHE cc_start: 0.8418 (t80) cc_final: 0.8206 (t80) REVERT: A 384 GLU cc_start: 0.8191 (tt0) cc_final: 0.7852 (pt0) REVERT: C 429 LEU cc_start: 0.8148 (mt) cc_final: 0.7932 (mm) REVERT: C 437 PHE cc_start: 0.8330 (t80) cc_final: 0.8028 (t80) REVERT: L 75 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7794 (mm) REVERT: L 85 THR cc_start: 0.7567 (m) cc_final: 0.6891 (p) REVERT: K 24 LYS cc_start: 0.8451 (mptt) cc_final: 0.8043 (mptt) REVERT: K 34 SER cc_start: 0.9005 (m) cc_final: 0.8762 (m) REVERT: K 42 GLN cc_start: 0.8160 (mp10) cc_final: 0.7580 (mp10) REVERT: K 74 ASN cc_start: 0.8302 (p0) cc_final: 0.7419 (m-40) REVERT: J 59 TYR cc_start: 0.7066 (m-80) cc_final: 0.6557 (m-80) outliers start: 59 outliers final: 45 residues processed: 235 average time/residue: 0.1134 time to fit residues: 38.7801 Evaluate side-chains 225 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 87 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 30 VAL Chi-restraints excluded: chain C residue 33 LEU 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 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 69 PHE Chi-restraints excluded: chain H residue 76 ASN 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 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 19 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 151 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN B 355 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.122990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081868 restraints weight = 46785.597| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.52 r_work: 0.3039 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1293 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= 0.145 Angle : 0.541 9.024 20796 Z= 0.277 Chirality : 0.042 0.240 2282 Planarity : 0.003 0.031 2643 Dihedral : 4.789 56.221 2012 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 3.92 % Allowed : 22.39 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1832 helix: 2.09 (0.27), residues: 326 sheet: 0.20 (0.25), residues: 445 loop : -0.42 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.018 0.001 TYR K 49 PHE 0.023 0.001 PHE A 111 TRP 0.013 0.001 TRP H 103 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (15261) covalent geometry : angle 0.52981 / 0.27 (20683) SS BOND : bond 0.00342 / 0.23 ( 22) SS BOND : angle 0.88844 / 0.67 ( 44) hydrogen bonds : bond 0.03584 / 2.45 ( 546) hydrogen bonds : angle 5.24418 / 3.69 ( 1539) link_ALPHA1-3 : bond 0.00248 / 0.13 ( 2) link_ALPHA1-3 : angle 1.51490 / 0.76 ( 6) link_BETA1-4 : bond 0.00428 / 0.21 ( 7) link_BETA1-4 : angle 1.51429 / 1.17 ( 21) link_NAG-ASN : bond 0.00438 / 0.25 ( 14) link_NAG-ASN : angle 2.12713 / 1.22 ( 42) *********************** 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 254 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7790 (mtp85) REVERT: B 314 MET cc_start: 0.7756 (mmt) cc_final: 0.7543 (mmp) REVERT: B 352 HIS cc_start: 0.7410 (t70) cc_final: 0.7168 (t70) REVERT: A 384 GLU cc_start: 0.8220 (tt0) cc_final: 0.7866 (pt0) REVERT: C 437 PHE cc_start: 0.8383 (t80) cc_final: 0.8111 (t80) REVERT: L 75 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7871 (mm) REVERT: L 85 THR cc_start: 0.7499 (m) cc_final: 0.6776 (p) REVERT: H 62 ARG cc_start: 0.8398 (mmt90) cc_final: 0.8192 (mmt90) REVERT: K 11 LEU cc_start: 0.8771 (tp) cc_final: 0.8420 (tp) REVERT: K 34 SER cc_start: 0.9010 (m) cc_final: 0.8778 (m) REVERT: K 42 GLN cc_start: 0.8196 (mp10) cc_final: 0.7652 (mp-120) REVERT: K 61 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6719 (ptp-110) REVERT: K 74 ASN cc_start: 0.8272 (p0) cc_final: 0.7317 (m-40) REVERT: J 59 TYR cc_start: 0.7031 (m-80) cc_final: 0.6480 (m-80) outliers start: 63 outliers final: 51 residues processed: 236 average time/residue: 0.1093 time to fit residues: 37.5937 Evaluate side-chains 235 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 87 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 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 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 69 PHE 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 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 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN 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 = 0.122945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082388 restraints weight = 46827.400| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.48 r_work: 0.3040 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- 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 = 0.50 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15306 Z= 0.155 Angle : 0.545 8.340 20796 Z= 0.278 Chirality : 0.042 0.221 2282 Planarity : 0.003 0.032 2643 Dihedral : 4.763 55.550 2012 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 3.92 % Allowed : 22.45 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1832 helix: 2.05 (0.27), residues: 327 sheet: 0.22 (0.25), residues: 445 loop : -0.42 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.015 0.001 TYR K 49 PHE 0.024 0.001 PHE A 111 TRP 0.012 0.001 TRP H 103 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (15261) covalent geometry : angle 0.53289 / 0.28 (20683) SS BOND : bond 0.00314 / 0.23 ( 22) SS BOND : angle 1.07823 / 0.85 ( 44) hydrogen bonds : bond 0.03496 / 2.39 ( 546) hydrogen bonds : angle 5.15315 / 3.63 ( 1539) link_ALPHA1-3 : bond 0.00203 / 0.10 ( 2) link_ALPHA1-3 : angle 1.49799 / 0.75 ( 6) link_BETA1-4 : bond 0.00414 / 0.21 ( 7) link_BETA1-4 : angle 1.49447 / 1.17 ( 21) link_NAG-ASN : bond 0.00420 / 0.25 ( 14) link_NAG-ASN : angle 2.10142 / 1.21 ( 42) *********************** 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 253 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 MET cc_start: 0.6858 (ppp) cc_final: 0.6580 (ppp) REVERT: A 384 GLU cc_start: 0.8168 (tt0) cc_final: 0.7818 (pt0) REVERT: C 344 MET cc_start: 0.5199 (tmm) cc_final: 0.4896 (tmm) REVERT: C 438 HIS cc_start: 0.8413 (m90) cc_final: 0.7774 (m90) REVERT: L 75 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7925 (mm) REVERT: L 85 THR cc_start: 0.7494 (m) cc_final: 0.6819 (p) REVERT: H 62 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8149 (mmt90) REVERT: K 11 LEU cc_start: 0.8809 (tp) cc_final: 0.8543 (tp) REVERT: K 24 LYS cc_start: 0.8366 (mptt) cc_final: 0.7983 (ttpp) REVERT: K 34 SER cc_start: 0.9012 (m) cc_final: 0.8780 (m) REVERT: K 42 GLN cc_start: 0.8184 (mp10) cc_final: 0.7628 (mp10) REVERT: K 53 LYS cc_start: 0.8127 (mptt) cc_final: 0.7623 (mtmt) REVERT: K 61 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6796 (ptp-110) REVERT: K 74 ASN cc_start: 0.8271 (p0) cc_final: 0.7364 (m-40) REVERT: J 59 TYR cc_start: 0.7103 (m-80) cc_final: 0.6458 (m-80) outliers start: 63 outliers final: 56 residues processed: 234 average time/residue: 0.1356 time to fit residues: 46.4959 Evaluate side-chains 244 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 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 87 ASN 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 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 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 77 THR 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 86 ASP 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 97 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 107 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084441 restraints weight = 34201.710| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.02 r_work: 0.3087 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15306 Z= 0.113 Angle : 0.533 7.778 20796 Z= 0.272 Chirality : 0.042 0.232 2282 Planarity : 0.003 0.073 2643 Dihedral : 4.682 55.809 2012 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.54 % Rotamer: Outliers : 3.67 % Allowed : 23.13 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1832 helix: 2.08 (0.27), residues: 327 sheet: 0.26 (0.25), residues: 445 loop : -0.39 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.012 0.001 TYR B 349 PHE 0.020 0.001 PHE B 111 TRP 0.011 0.001 TRP H 103 HIS 0.003 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (15261) covalent geometry : angle 0.52217 / 0.27 (20683) SS BOND : bond 0.00432 / 0.21 ( 22) SS BOND : angle 0.97250 / 0.79 ( 44) hydrogen bonds : bond 0.03284 / 2.25 ( 546) hydrogen bonds : angle 5.01787 / 3.55 ( 1539) link_ALPHA1-3 : bond 0.00311 / 0.16 ( 2) link_ALPHA1-3 : angle 1.47176 / 0.74 ( 6) link_BETA1-4 : bond 0.00421 / 0.21 ( 7) link_BETA1-4 : angle 1.47117 / 1.15 ( 21) link_NAG-ASN : bond 0.00395 / 0.21 ( 14) link_NAG-ASN : angle 2.05966 / 1.18 ( 42) *********************** 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 249 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.6685 (t70) REVERT: B 352 HIS cc_start: 0.7349 (t70) cc_final: 0.7040 (t70) REVERT: A 384 GLU cc_start: 0.8147 (tt0) cc_final: 0.7813 (pt0) REVERT: C 344 MET cc_start: 0.5172 (tmm) cc_final: 0.4841 (tmm) REVERT: C 438 HIS cc_start: 0.8488 (m90) cc_final: 0.7872 (m90) REVERT: L 75 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7921 (mm) REVERT: L 85 THR cc_start: 0.7525 (m) cc_final: 0.6823 (p) REVERT: K 11 LEU cc_start: 0.8797 (tp) cc_final: 0.8525 (tp) REVERT: K 34 SER cc_start: 0.9005 (m) cc_final: 0.8782 (m) REVERT: K 42 GLN cc_start: 0.8183 (mp10) cc_final: 0.7629 (mp10) REVERT: K 53 LYS cc_start: 0.8203 (mptt) cc_final: 0.8000 (mptt) REVERT: K 61 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6803 (ptp-110) REVERT: K 74 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7311 (m-40) REVERT: J 3 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7809 (tm-30) REVERT: J 5 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8118 (tp40) outliers start: 59 outliers final: 50 residues processed: 232 average time/residue: 0.1233 time to fit residues: 41.7962 Evaluate side-chains 238 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 30 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 ASN 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 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 77 THR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 25 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 4 optimal weight: 0.0970 chunk 161 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 60 optimal weight: 0.0030 chunk 148 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.124158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084655 restraints weight = 38742.166| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.20 r_work: 0.3087 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15306 Z= 0.105 Angle : 0.526 9.819 20796 Z= 0.268 Chirality : 0.041 0.229 2282 Planarity : 0.003 0.061 2643 Dihedral : 4.603 55.799 2010 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 3.86 % Allowed : 22.95 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1832 helix: 2.17 (0.27), residues: 327 sheet: 0.33 (0.25), residues: 441 loop : -0.34 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.018 0.001 TYR K 49 PHE 0.019 0.001 PHE B 111 TRP 0.011 0.001 TRP H 33 HIS 0.003 0.000 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (15261) covalent geometry : angle 0.51503 / 0.27 (20683) SS BOND : bond 0.00232 / 0.16 ( 22) SS BOND : angle 1.01619 / 0.77 ( 44) hydrogen bonds : bond 0.03175 / 2.19 ( 546) hydrogen bonds : angle 4.90335 / 3.47 ( 1539) link_ALPHA1-3 : bond 0.00287 / 0.15 ( 2) link_ALPHA1-3 : angle 1.43830 / 0.73 ( 6) link_BETA1-4 : bond 0.00451 / 0.22 ( 7) link_BETA1-4 : angle 1.44986 / 1.13 ( 21) link_NAG-ASN : bond 0.00387 / 0.21 ( 14) link_NAG-ASN : angle 2.01295 / 1.15 ( 42) *********************** 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 255 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.6612 (t70) REVERT: B 314 MET cc_start: 0.7839 (mmp) cc_final: 0.7620 (mpp) REVERT: B 352 HIS cc_start: 0.7334 (t70) cc_final: 0.7050 (t70) REVERT: A 384 GLU cc_start: 0.8023 (tt0) cc_final: 0.7712 (pt0) REVERT: C 344 MET cc_start: 0.5165 (tmm) cc_final: 0.4834 (tmm) REVERT: C 437 PHE cc_start: 0.8452 (t80) cc_final: 0.8149 (t80) REVERT: C 438 HIS cc_start: 0.8282 (m90) cc_final: 0.7638 (m90) REVERT: L 75 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7964 (mm) REVERT: L 85 THR cc_start: 0.7562 (m) cc_final: 0.6869 (p) REVERT: H 38 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6841 (pttt) REVERT: K 11 LEU cc_start: 0.8817 (tp) cc_final: 0.8573 (tp) REVERT: K 34 SER cc_start: 0.8966 (m) cc_final: 0.8729 (m) REVERT: K 42 GLN cc_start: 0.8205 (mp10) cc_final: 0.7640 (mp10) REVERT: K 61 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6832 (ptp-110) REVERT: K 74 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7299 (m-40) REVERT: J 3 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7787 (tm-30) REVERT: J 5 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8133 (tp40) outliers start: 62 outliers final: 51 residues processed: 237 average time/residue: 0.1267 time to fit residues: 43.6743 Evaluate side-chains 241 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 416 LEU 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 87 ASN 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 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 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 51 ILE Chi-restraints excluded: chain H residue 77 THR 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 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 91 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.121898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080361 restraints weight = 53976.717| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.74 r_work: 0.3002 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 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 = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15306 Z= 0.228 Angle : 0.591 8.207 20796 Z= 0.301 Chirality : 0.044 0.217 2282 Planarity : 0.004 0.056 2643 Dihedral : 4.810 53.744 2010 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 3.79 % Allowed : 23.20 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1832 helix: 2.04 (0.27), residues: 327 sheet: 0.17 (0.25), residues: 442 loop : -0.40 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 74 TYR 0.021 0.001 TYR K 49 PHE 0.029 0.002 PHE A 111 TRP 0.017 0.001 TRP B 60 HIS 0.005 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (15261) covalent geometry : angle 0.57976 / 0.30 (20683) SS BOND : bond 0.00402 / 0.30 ( 22) SS BOND : angle 1.08687 / 0.85 ( 44) hydrogen bonds : bond 0.03581 / 2.45 ( 546) hydrogen bonds : angle 5.13418 / 3.62 ( 1539) link_ALPHA1-3 : bond 0.00123 / 0.06 ( 2) link_ALPHA1-3 : angle 1.57480 / 0.78 ( 6) link_BETA1-4 : bond 0.00465 / 0.24 ( 7) link_BETA1-4 : angle 1.51902 / 1.18 ( 21) link_NAG-ASN : bond 0.00457 / 0.29 ( 14) link_NAG-ASN : angle 2.09664 / 1.23 ( 42) *********************** 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 250 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.6677 (t70) REVERT: B 74 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.7948 (mtp85) REVERT: B 352 HIS cc_start: 0.7340 (t70) cc_final: 0.7057 (t70) REVERT: B 386 MET cc_start: 0.6901 (ppp) cc_final: 0.6495 (ppp) REVERT: A 384 GLU cc_start: 0.8051 (tt0) cc_final: 0.7731 (pt0) REVERT: C 344 MET cc_start: 0.5296 (tmm) cc_final: 0.4917 (tmm) REVERT: C 437 PHE cc_start: 0.8493 (t80) cc_final: 0.8199 (t80) REVERT: C 438 HIS cc_start: 0.8439 (m90) cc_final: 0.7804 (m90) REVERT: L 75 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8006 (mm) REVERT: L 85 THR cc_start: 0.7499 (m) cc_final: 0.6809 (p) REVERT: H 38 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6872 (pttt) REVERT: K 42 GLN cc_start: 0.8152 (mp10) cc_final: 0.7592 (mp10) REVERT: K 61 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6934 (ptp-110) REVERT: K 74 ASN cc_start: 0.8408 (p0) cc_final: 0.7365 (m-40) REVERT: J 3 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7444 (tm-30) REVERT: J 5 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8167 (tp40) outliers start: 61 outliers final: 55 residues processed: 232 average time/residue: 0.1378 time to fit residues: 46.1268 Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 111 PHE Chi-restraints excluded: chain B residue 128 THR 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 87 ASN 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 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 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 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 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 160 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 176 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN 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 = 0.122388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082685 restraints weight = 37491.150| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.10 r_work: 0.3039 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 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 = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15306 Z= 0.202 Angle : 0.594 9.123 20796 Z= 0.303 Chirality : 0.043 0.238 2282 Planarity : 0.004 0.050 2643 Dihedral : 4.836 52.648 2010 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 4.10 % Allowed : 23.07 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1832 helix: 1.98 (0.28), residues: 326 sheet: 0.19 (0.26), residues: 436 loop : -0.46 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 74 TYR 0.020 0.001 TYR K 49 PHE 0.027 0.002 PHE A 111 TRP 0.014 0.001 TRP H 103 HIS 0.005 0.001 HIS J 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (15261) covalent geometry : angle 0.58360 / 0.30 (20683) SS BOND : bond 0.00369 / 0.28 ( 22) SS BOND : angle 1.02431 / 0.81 ( 44) hydrogen bonds : bond 0.03485 / 2.40 ( 546) hydrogen bonds : angle 5.13524 / 3.62 ( 1539) link_ALPHA1-3 : bond 0.00144 / 0.08 ( 2) link_ALPHA1-3 : angle 1.52969 / 0.77 ( 6) link_BETA1-4 : bond 0.00486 / 0.24 ( 7) link_BETA1-4 : angle 1.46661 / 1.13 ( 21) link_NAG-ASN : bond 0.00434 / 0.27 ( 14) link_NAG-ASN : angle 2.08280 / 1.22 ( 42) *********************** 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 257 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.6641 (t70) REVERT: B 74 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.8028 (mtp85) REVERT: B 361 TYR cc_start: 0.3903 (OUTLIER) cc_final: 0.1221 (t80) REVERT: B 386 MET cc_start: 0.6976 (ppp) cc_final: 0.6546 (ppp) REVERT: A 86 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: A 375 ILE cc_start: 0.6187 (mm) cc_final: 0.5885 (mm) REVERT: A 384 GLU cc_start: 0.8031 (tt0) cc_final: 0.7719 (pt0) REVERT: C 344 MET cc_start: 0.5089 (tmm) cc_final: 0.4761 (tmm) REVERT: C 437 PHE cc_start: 0.8493 (t80) cc_final: 0.8209 (t80) REVERT: C 438 HIS cc_start: 0.8458 (m90) cc_final: 0.7816 (m90) REVERT: L 75 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7991 (mm) REVERT: L 85 THR cc_start: 0.7475 (m) cc_final: 0.6806 (p) REVERT: H 38 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6776 (pttt) REVERT: K 42 GLN cc_start: 0.8084 (mp10) cc_final: 0.7538 (mp10) REVERT: K 53 LYS cc_start: 0.8184 (mptt) cc_final: 0.7906 (mptt) REVERT: K 61 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6904 (ptp-110) REVERT: K 74 ASN cc_start: 0.8362 (p0) cc_final: 0.7317 (m-40) REVERT: J 3 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7459 (tm-30) outliers start: 66 outliers final: 56 residues processed: 239 average time/residue: 0.1403 time to fit residues: 48.5641 Evaluate side-chains 251 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 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 87 ASN 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 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 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 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 47 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 chunk 58 optimal weight: 0.0060 chunk 178 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.123985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082936 restraints weight = 48126.945| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.59 r_work: 0.3055 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15306 Z= 0.105 Angle : 0.557 9.446 20796 Z= 0.284 Chirality : 0.042 0.234 2282 Planarity : 0.003 0.046 2643 Dihedral : 4.678 53.591 2010 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.38 % Rotamer: Outliers : 3.61 % Allowed : 23.63 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1832 helix: 2.13 (0.28), residues: 326 sheet: 0.22 (0.26), residues: 432 loop : -0.39 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 40 TYR 0.016 0.001 TYR K 49 PHE 0.019 0.001 PHE B 111 TRP 0.011 0.001 TRP H 103 HIS 0.004 0.001 HIS J 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15261) covalent geometry : angle 0.54660 / 0.28 (20683) SS BOND : bond 0.00219 / 0.16 ( 22) SS BOND : angle 0.90213 / 0.70 ( 44) hydrogen bonds : bond 0.03176 / 2.21 ( 546) hydrogen bonds : angle 4.92708 / 3.48 ( 1539) link_ALPHA1-3 : bond 0.00268 / 0.14 ( 2) link_ALPHA1-3 : angle 1.45086 / 0.73 ( 6) link_BETA1-4 : bond 0.00401 / 0.19 ( 7) link_BETA1-4 : angle 1.44555 / 1.14 ( 21) link_NAG-ASN : bond 0.00387 / 0.21 ( 14) link_NAG-ASN : angle 2.02829 / 1.18 ( 42) ********************** 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 250 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7418 (t70) REVERT: B 21 GLU cc_start: 0.5975 (pm20) cc_final: 0.5523 (pm20) REVERT: B 74 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7849 (mtp85) REVERT: B 314 MET cc_start: 0.7782 (mmp) cc_final: 0.7434 (mpp) REVERT: B 361 TYR cc_start: 0.3728 (OUTLIER) cc_final: 0.1243 (t80) REVERT: B 386 MET cc_start: 0.6854 (ppp) cc_final: 0.6461 (ppp) REVERT: B 460 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5520 (mm) REVERT: A 384 GLU cc_start: 0.8090 (tt0) cc_final: 0.7761 (pt0) REVERT: C 344 MET cc_start: 0.4999 (tmm) cc_final: 0.4693 (tmm) REVERT: C 437 PHE cc_start: 0.8450 (t80) cc_final: 0.8167 (t80) REVERT: C 438 HIS cc_start: 0.8286 (m90) cc_final: 0.7654 (m90) REVERT: L 45 LYS cc_start: 0.7971 (tptp) cc_final: 0.7685 (tptp) REVERT: L 75 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7804 (mm) REVERT: L 85 THR cc_start: 0.7493 (m) cc_final: 0.6787 (p) REVERT: H 38 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6724 (pttt) REVERT: K 42 GLN cc_start: 0.8155 (mp10) cc_final: 0.7620 (mp10) REVERT: K 53 LYS cc_start: 0.8177 (mptt) cc_final: 0.7866 (mptt) REVERT: K 61 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6837 (ptp-110) REVERT: K 74 ASN cc_start: 0.8377 (p0) cc_final: 0.7332 (m-40) REVERT: J 3 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7436 (tm-30) REVERT: J 5 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8163 (tp40) REVERT: J 19 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8498 (mmmm) REVERT: J 35 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8425 (mp0) outliers start: 58 outliers final: 49 residues processed: 232 average time/residue: 0.1374 time to fit residues: 45.9566 Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 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 87 ASN 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 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 108 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 192 TYR 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 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 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 47 LEU 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 7 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS A 273 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082957 restraints weight = 41641.266| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.32 r_work: 0.3065 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1778 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= 0.129 Angle : 0.556 9.459 20796 Z= 0.284 Chirality : 0.042 0.236 2282 Planarity : 0.003 0.043 2643 Dihedral : 4.646 53.626 2010 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 3.79 % Allowed : 23.63 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1832 helix: 2.09 (0.27), residues: 326 sheet: 0.27 (0.26), residues: 432 loop : -0.38 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 40 TYR 0.019 0.001 TYR K 49 PHE 0.021 0.001 PHE B 111 TRP 0.009 0.001 TRP H 103 HIS 0.003 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15261) covalent geometry : angle 0.54615 / 0.28 (20683) SS BOND : bond 0.00274 / 0.20 ( 22) SS BOND : angle 0.92591 / 0.73 ( 44) hydrogen bonds : bond 0.03207 / 2.22 ( 546) hydrogen bonds : angle 4.89669 / 3.46 ( 1539) link_ALPHA1-3 : bond 0.00268 / 0.14 ( 2) link_ALPHA1-3 : angle 1.46211 / 0.74 ( 6) link_BETA1-4 : bond 0.00426 / 0.22 ( 7) link_BETA1-4 : angle 1.44877 / 1.13 ( 21) link_NAG-ASN : bond 0.00380 / 0.22 ( 14) link_NAG-ASN : angle 2.01218 / 1.18 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.29 seconds wall clock time: 78 minutes 31.60 seconds (4711.60 seconds total)