Starting phenix.real_space_refine on Fri Sep 11 09:00:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kkt_0702/09_2026/6kkt_0702.map" } resolution = 2.9 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 Cl 4 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" 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: "D" 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: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" 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: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8416 At special positions: 0 Unit cell: (78.11, 101.65, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " 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=4, symmetry=0 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC I 1 " - " GLC I 2 " " BGC J 1 " - " GLC J 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 312 " " NAG H 1 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 275.8 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 70.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.745A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 176 removed outlier: 6.953A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 4.266A pdb=" N PHE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.648A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 269 removed outlier: 3.523A pdb=" N THR A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.560A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.596A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.638A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.613A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.513A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.575A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.412A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 537 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 4.889A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.506A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 removed outlier: 3.593A pdb=" N ALA A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 4.038A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.557A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.745A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 176 removed outlier: 6.954A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 4.267A pdb=" N PHE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.649A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 269 removed outlier: 3.523A pdb=" N THR B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 276 through 298 removed outlier: 3.560A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.597A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.638A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.614A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.513A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.576A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.413A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 504 through 537 Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 4.889A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.506A pdb=" N LEU B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.593A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 4.038A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.558A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 328 494 hydrogen bonds defined for protein. 1434 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: 1.23 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2474 1.35 - 1.48: 2385 1.48 - 1.60: 3663 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 8626 Sorted by residual: bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.410 1.503 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.410 1.503 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 BGC E 1 " pdb=" O5 BGC E 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BGC J 1 " pdb=" O5 BGC J 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.410 1.485 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 11029 2.06 - 4.13: 598 4.13 - 6.19: 121 6.19 - 8.26: 37 8.26 - 10.32: 9 Bond angle restraints: 11794 Sorted by residual: angle pdb=" N VAL B 431 " pdb=" CA VAL B 431 " pdb=" C VAL B 431 " ideal model delta sigma weight residual 113.43 107.83 5.60 1.09e+00 8.42e-01 2.64e+01 angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 113.43 107.83 5.60 1.09e+00 8.42e-01 2.64e+01 angle pdb=" C VAL A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta sigma weight residual 122.08 127.25 -5.17 1.47e+00 4.63e-01 1.24e+01 angle pdb=" C VAL B 490 " pdb=" N SER B 491 " pdb=" CA SER B 491 " ideal model delta sigma weight residual 122.08 127.24 -5.16 1.47e+00 4.63e-01 1.23e+01 angle pdb=" CA PRO A 230 " pdb=" C PRO A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 117.93 122.12 -4.19 1.20e+00 6.94e-01 1.22e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 4873 34.22 - 68.43: 33 68.43 - 102.65: 2 102.65 - 136.86: 2 136.86 - 171.08: 2 Dihedral angle restraints: 4912 sinusoidal: 1830 harmonic: 3082 Sorted by residual: dihedral pdb=" C26 DU0 A2000 " pdb=" C24 DU0 A2000 " pdb=" C25 DU0 A2000 " pdb=" O23 DU0 A2000 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C26 DU0 B2000 " pdb=" C24 DU0 B2000 " pdb=" C25 DU0 B2000 " pdb=" O23 DU0 B2000 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA VAL A 490 " pdb=" C VAL A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 4909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1239 0.086 - 0.173: 211 0.173 - 0.259: 12 0.259 - 0.345: 2 0.345 - 0.432: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.38e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.60e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 230 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 231 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 230 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO B 231 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO B 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.036 5.00e-02 4.00e+02 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.90: 3212 2.90 - 3.46: 9186 3.46 - 4.02: 15199 4.02 - 4.58: 21702 4.58 - 5.14: 31072 Nonbonded interactions: 80371 Sorted by model distance: nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.343 3.040 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.345 3.040 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 3.040 nonbonded pdb=" O2 GLC I 2 " pdb=" O4 GLC I 2 " model vdw 2.383 3.040 nonbonded pdb=" N ASP B 354 " pdb=" OD1 ASP B 354 " model vdw 2.396 3.120 ... (remaining 80366 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.011 0.103 8648 Z= 0.451 Angle : 1.258 17.451 11842 Z= 0.641 Chirality : 0.065 0.432 1466 Planarity : 0.008 0.070 1404 Dihedral : 11.165 171.079 2926 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.34 % Allowed : 2.49 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.62 (0.20), residues: 1070 helix: -2.23 (0.15), residues: 680 sheet: None (None), residues: 0 loop : -2.43 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 252 TYR 0.028 0.003 TYR B 466 PHE 0.038 0.004 PHE B 473 TRP 0.026 0.003 TRP B 339 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.45 ( 8626) covalent geometry : angle 1.16547 / 0.62 (11794) SS BOND : bond 0.00361 / 0.21 ( 6) SS BOND : angle 2.68606 / 1.39 ( 12) hydrogen bonds : bond 0.21045 / 14.11 ( 494) hydrogen bonds : angle 6.81479 / 5.03 ( 1434) Misc. bond : bond 0.00749 / 0.44 ( 4) link_ALPHA1-4 : bond 0.05558 / 3.29 ( 4) link_ALPHA1-4 : angle 2.30409 / 1.29 ( 12) link_BETA1-4 : bond 0.01666 / 1.02 ( 4) link_BETA1-4 : angle 10.98747 / 6.06 ( 12) link_NAG-ASN : bond 0.01196 / 0.71 ( 4) link_NAG-ASN : angle 9.71865 / 6.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 0.334 Fit side-chains REVERT: A 190 SER cc_start: 0.8834 (t) cc_final: 0.8254 (p) REVERT: A 275 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7793 (tttp) REVERT: A 553 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7687 (tt0) REVERT: B 190 SER cc_start: 0.8809 (t) cc_final: 0.8163 (p) REVERT: B 275 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7939 (tttp) outliers start: 3 outliers final: 2 residues processed: 219 average time/residue: 0.5648 time to fit residues: 131.6498 Evaluate side-chains 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 ASN A 547 HIS A 615 HIS B 547 HIS B 551 ASN B 615 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.089821 restraints weight = 10976.054| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.39 r_work: 0.2806 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8648 Z= 0.139 Angle : 0.719 11.458 11842 Z= 0.333 Chirality : 0.045 0.231 1466 Planarity : 0.005 0.046 1404 Dihedral : 10.370 159.018 1198 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.42 % Allowed : 9.75 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.24), residues: 1070 helix: 0.15 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 543 TYR 0.010 0.001 TYR A 651 PHE 0.015 0.001 PHE A 341 TRP 0.009 0.001 TRP A 381 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8626) covalent geometry : angle 0.66156 / 0.32 (11794) SS BOND : bond 0.00236 / 0.14 ( 6) SS BOND : angle 1.60080 / 0.82 ( 12) hydrogen bonds : bond 0.05243 / 3.54 ( 494) hydrogen bonds : angle 4.30606 / 3.10 ( 1434) Misc. bond : bond 0.00070 / 0.04 ( 4) link_ALPHA1-4 : bond 0.00235 / 0.14 ( 4) link_ALPHA1-4 : angle 1.47003 / 0.79 ( 12) link_BETA1-4 : bond 0.00998 / 0.61 ( 4) link_BETA1-4 : angle 6.80671 / 3.65 ( 12) link_NAG-ASN : bond 0.00340 / 0.21 ( 4) link_NAG-ASN : angle 5.33423 / 3.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.331 Fit side-chains REVERT: A 179 VAL cc_start: 0.8396 (t) cc_final: 0.8114 (p) REVERT: A 180 VAL cc_start: 0.9149 (t) cc_final: 0.8949 (p) REVERT: A 190 SER cc_start: 0.8861 (t) cc_final: 0.8244 (p) REVERT: A 435 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8218 (mmp) REVERT: A 531 GLN cc_start: 0.8505 (tp40) cc_final: 0.8296 (tt0) REVERT: A 553 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7727 (tt0) REVERT: A 583 MET cc_start: 0.9140 (tpp) cc_final: 0.8916 (mmm) REVERT: B 322 ILE cc_start: 0.8940 (tt) cc_final: 0.8455 (mt) REVERT: B 376 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8860 (tp) REVERT: B 583 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (mmm) outliers start: 39 outliers final: 6 residues processed: 170 average time/residue: 0.6415 time to fit residues: 115.3488 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 537 ASN B 319 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.088375 restraints weight = 10841.542| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.38 r_work: 0.2803 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8648 Z= 0.144 Angle : 0.663 10.412 11842 Z= 0.309 Chirality : 0.043 0.189 1466 Planarity : 0.004 0.043 1404 Dihedral : 9.307 142.267 1194 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.20 % Allowed : 12.02 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.25), residues: 1070 helix: 1.17 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 528 TYR 0.021 0.002 TYR A 651 PHE 0.011 0.002 PHE B 428 TRP 0.010 0.001 TRP A 381 HIS 0.002 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 8626) covalent geometry : angle 0.61392 / 0.30 (11794) SS BOND : bond 0.00272 / 0.16 ( 6) SS BOND : angle 1.51503 / 0.76 ( 12) hydrogen bonds : bond 0.04561 / 3.07 ( 494) hydrogen bonds : angle 3.93072 / 2.81 ( 1434) Misc. bond : bond 0.00038 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00456 / 0.28 ( 4) link_ALPHA1-4 : angle 1.12887 / 0.62 ( 12) link_BETA1-4 : bond 0.00954 / 0.59 ( 4) link_BETA1-4 : angle 6.14930 / 3.29 ( 12) link_NAG-ASN : bond 0.00028 / 0.02 ( 4) link_NAG-ASN : angle 4.73260 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.326 Fit side-chains REVERT: A 179 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 190 SER cc_start: 0.8921 (t) cc_final: 0.8324 (p) REVERT: A 435 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8195 (mmp) REVERT: A 566 GLU cc_start: 0.9376 (tp30) cc_final: 0.9158 (tp30) REVERT: B 179 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8194 (p) REVERT: B 492 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8738 (mmt180) outliers start: 37 outliers final: 8 residues processed: 158 average time/residue: 0.6563 time to fit residues: 109.5276 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 492 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 0.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 319 GLN A 439 ASN A 531 GLN A 537 ASN B 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.090384 restraints weight = 11085.389| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.43 r_work: 0.2835 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8648 Z= 0.112 Angle : 0.612 9.922 11842 Z= 0.284 Chirality : 0.042 0.169 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.075 137.939 1194 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.08 % Allowed : 11.90 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.26), residues: 1070 helix: 1.77 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 528 TYR 0.016 0.001 TYR B 651 PHE 0.008 0.001 PHE A 467 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 8626) covalent geometry : angle 0.56725 / 0.27 (11794) SS BOND : bond 0.00178 / 0.10 ( 6) SS BOND : angle 1.18171 / 0.58 ( 12) hydrogen bonds : bond 0.03810 / 2.55 ( 494) hydrogen bonds : angle 3.74498 / 2.68 ( 1434) Misc. bond : bond 0.00023 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00405 / 0.24 ( 4) link_ALPHA1-4 : angle 1.27915 / 0.76 ( 12) link_BETA1-4 : bond 0.01112 / 0.69 ( 4) link_BETA1-4 : angle 5.76264 / 3.07 ( 12) link_NAG-ASN : bond 0.00274 / 0.16 ( 4) link_NAG-ASN : angle 4.12013 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.266 Fit side-chains REVERT: A 179 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 190 SER cc_start: 0.8938 (t) cc_final: 0.8307 (p) REVERT: A 191 ARG cc_start: 0.8797 (mpt180) cc_final: 0.8561 (mpt180) REVERT: A 435 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8178 (mmp) REVERT: B 122 MET cc_start: 0.8868 (tpp) cc_final: 0.8580 (mmm) REVERT: B 179 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 190 SER cc_start: 0.8972 (t) cc_final: 0.8336 (p) REVERT: B 378 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: B 386 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7900 (tp30) outliers start: 36 outliers final: 10 residues processed: 159 average time/residue: 0.5962 time to fit residues: 100.4807 Evaluate side-chains 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 319 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 439 ASN B 551 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089220 restraints weight = 11083.319| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.43 r_work: 0.2825 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.200 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.63 % Allowed : 13.61 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66285 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26230 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 190 SER cc_start: 0.8950 (t) cc_final: 0.8335 (p) REVERT: A 435 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8176 (mmp) REVERT: B 122 MET cc_start: 0.8825 (tpp) cc_final: 0.8537 (mmm) REVERT: B 179 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 378 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8531 (mt-10) REVERT: B 386 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7908 (tp30) outliers start: 32 outliers final: 15 residues processed: 143 average time/residue: 0.6808 time to fit residues: 102.7599 Evaluate side-chains 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 537 ASN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089250 restraints weight = 10983.264| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.41 r_work: 0.2827 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.199 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66287 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26226 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 190 SER cc_start: 0.8924 (t) cc_final: 0.8333 (p) REVERT: A 435 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8169 (mmp) REVERT: B 122 MET cc_start: 0.8824 (tpp) cc_final: 0.8538 (mmm) REVERT: B 179 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 378 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8523 (mt-10) REVERT: B 386 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7904 (tp30) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.7265 time to fit residues: 102.4667 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 537 ASN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089187 restraints weight = 11086.791| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.43 r_work: 0.2825 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.199 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66287 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26226 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 190 SER cc_start: 0.8923 (t) cc_final: 0.8333 (p) REVERT: A 435 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8173 (mmp) REVERT: B 122 MET cc_start: 0.8827 (tpp) cc_final: 0.8540 (mmm) REVERT: B 179 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 378 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8526 (mt-10) REVERT: B 386 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7915 (tp30) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.7278 time to fit residues: 101.7461 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 537 ASN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.089278 restraints weight = 10969.804| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.41 r_work: 0.2819 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.199 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66287 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26226 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 190 SER cc_start: 0.8922 (t) cc_final: 0.8332 (p) REVERT: A 435 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8172 (mmp) REVERT: B 122 MET cc_start: 0.8825 (tpp) cc_final: 0.8538 (mmm) REVERT: B 179 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 378 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8526 (mt-10) REVERT: B 386 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7911 (tp30) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.6853 time to fit residues: 96.1044 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 18 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 537 ASN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089250 restraints weight = 10990.949| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.42 r_work: 0.2829 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.199 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66287 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26226 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8108 (p) REVERT: A 190 SER cc_start: 0.8924 (t) cc_final: 0.8333 (p) REVERT: A 435 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8169 (mmp) REVERT: B 122 MET cc_start: 0.8826 (tpp) cc_final: 0.8540 (mmm) REVERT: B 179 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 378 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: B 386 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7908 (tp30) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.7191 time to fit residues: 100.6658 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 537 ASN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089227 restraints weight = 11029.879| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.42 r_work: 0.2826 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.199 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66287 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26226 / 2.74 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 190 SER cc_start: 0.8923 (t) cc_final: 0.8332 (p) REVERT: A 435 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8170 (mmp) REVERT: B 122 MET cc_start: 0.8825 (tpp) cc_final: 0.8539 (mmm) REVERT: B 179 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8142 (p) REVERT: B 378 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: B 386 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7904 (tp30) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.7463 time to fit residues: 104.3440 Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 537 ASN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.089267 restraints weight = 10989.407| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.41 r_work: 0.2827 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8648 Z= 0.179 Angle : 0.997 59.199 11842 Z= 0.518 Chirality : 0.045 0.356 1466 Planarity : 0.004 0.037 1404 Dihedral : 9.060 136.654 1194 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1070 helix: 1.83 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.51 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.008 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8626) covalent geometry : angle 0.96493 / 0.51 (11794) SS BOND : bond 0.00357 / 0.19 ( 6) SS BOND : angle 1.34624 / 0.64 ( 12) hydrogen bonds : bond 0.03924 / 2.62 ( 494) hydrogen bonds : angle 3.75118 / 2.68 ( 1434) Misc. bond : bond 0.00035 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00367 / 0.22 ( 4) link_ALPHA1-4 : angle 1.32209 / 0.77 ( 12) link_BETA1-4 : bond 0.01717 / 0.94 ( 4) link_BETA1-4 : angle 6.66287 / 3.41 ( 12) link_NAG-ASN : bond 0.04021 / 2.01 ( 4) link_NAG-ASN : angle 4.26226 / 2.74 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.61 seconds wall clock time: 53 minutes 52.62 seconds (3232.62 seconds total)