Starting phenix.real_space_refine on Tue Mar 3 21:17:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kkt_0702/03_2026/6kkt_0702.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kkt_0702/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kkt_0702/03_2026/6kkt_0702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kkt_0702/03_2026/6kkt_0702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kkt_0702/03_2026/6kkt_0702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kkt_0702/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 2.27, per 1000 atoms: 0.27 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: 0.85 Conformation dependent library (CDL) restraints added in 431.4 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: 0.25 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: 1.31 Time building geometry restraints manager: 1.13 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 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+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 1.402 1.485 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 11009 2.06 - 4.13: 610 4.13 - 6.19: 133 6.19 - 8.26: 31 8.26 - 10.32: 11 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: 5237 34.22 - 68.43: 53 68.43 - 102.65: 42 102.65 - 136.86: 32 136.86 - 171.08: 2 Dihedral angle restraints: 5366 sinusoidal: 2284 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 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1233 0.086 - 0.173: 215 0.173 - 0.259: 14 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.030 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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= 0.453 Angle : 1.270 17.451 11842 Z= 0.644 Chirality : 0.066 0.432 1466 Planarity : 0.008 0.070 1404 Dihedral : 18.463 171.079 3380 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 covalent geometry : bond 0.01056 ( 8626) covalent geometry : angle 1.17772 (11794) SS BOND : bond 0.00361 ( 6) SS BOND : angle 2.68606 ( 12) hydrogen bonds : bond 0.21045 ( 494) hydrogen bonds : angle 6.81479 ( 1434) Misc. bond : bond 0.00749 ( 4) link_ALPHA1-4 : bond 0.05558 ( 4) link_ALPHA1-4 : angle 2.30409 ( 12) link_BETA1-4 : bond 0.01666 ( 4) link_BETA1-4 : angle 10.98747 ( 12) link_NAG-ASN : bond 0.01196 ( 4) link_NAG-ASN : angle 9.71865 ( 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 : 0.321 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: 0.5954 time to fit residues: 138.1809 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 : 0.357 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3417 r_free = 0.3417 target = 0.120919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.090551 restraints weight = 10965.846| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.39 r_work: 0.2829 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8648 Z= 0.139 Angle : 0.755 11.212 11842 Z= 0.341 Chirality : 0.044 0.211 1466 Planarity : 0.005 0.044 1404 Dihedral : 14.833 141.727 1652 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.74 % Allowed : 10.20 % Favored : 86.05 % 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: -0.86 (0.24), residues: 1070 helix: 0.25 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -2.02 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 543 TYR 0.013 0.001 TYR A 651 PHE 0.017 0.002 PHE A 341 TRP 0.009 0.001 TRP A 381 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8626) covalent geometry : angle 0.70167 (11794) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.70393 ( 12) hydrogen bonds : bond 0.04825 ( 494) hydrogen bonds : angle 4.21335 ( 1434) Misc. bond : bond 0.00069 ( 4) link_ALPHA1-4 : bond 0.01063 ( 4) link_ALPHA1-4 : angle 2.19686 ( 12) link_BETA1-4 : bond 0.00911 ( 4) link_BETA1-4 : angle 6.60425 ( 12) link_NAG-ASN : bond 0.00352 ( 4) link_NAG-ASN : angle 5.28899 ( 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 180 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.325 Fit side-chains REVERT: A 190 SER cc_start: 0.8877 (t) cc_final: 0.8284 (p) REVERT: A 275 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8069 (ttmm) REVERT: A 347 ASN cc_start: 0.8121 (t0) cc_final: 0.7437 (p0) REVERT: A 553 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7731 (tt0) REVERT: B 347 ASN cc_start: 0.8065 (t0) cc_final: 0.7262 (p0) REVERT: B 376 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8927 (tp) REVERT: B 387 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8492 (tttm) outliers start: 33 outliers final: 3 residues processed: 166 average time/residue: 0.6793 time to fit residues: 118.7607 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 387 LYS 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: 0.0670 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 319 GLN A 531 GLN A 537 ASN B 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.089016 restraints weight = 10810.908| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.39 r_work: 0.2815 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8648 Z= 0.137 Angle : 0.677 10.589 11842 Z= 0.310 Chirality : 0.043 0.184 1466 Planarity : 0.004 0.041 1404 Dihedral : 11.718 135.730 1648 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.08 % Allowed : 11.68 % Favored : 84.24 % 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: 0.30 (0.25), residues: 1070 helix: 1.24 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 528 TYR 0.019 0.002 TYR A 651 PHE 0.016 0.002 PHE B 258 TRP 0.010 0.001 TRP A 381 HIS 0.002 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8626) covalent geometry : angle 0.62243 (11794) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.40560 ( 12) hydrogen bonds : bond 0.04439 ( 494) hydrogen bonds : angle 3.89944 ( 1434) Misc. bond : bond 0.00045 ( 4) link_ALPHA1-4 : bond 0.00990 ( 4) link_ALPHA1-4 : angle 1.82348 ( 12) link_BETA1-4 : bond 0.00902 ( 4) link_BETA1-4 : angle 6.25872 ( 12) link_NAG-ASN : bond 0.00068 ( 4) link_NAG-ASN : angle 5.15108 ( 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 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.218 Fit side-chains REVERT: A 179 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8180 (p) REVERT: A 190 SER cc_start: 0.8935 (t) cc_final: 0.8318 (p) REVERT: A 275 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7998 (ttmm) REVERT: A 566 GLU cc_start: 0.9381 (tp30) cc_final: 0.9165 (tp30) REVERT: B 179 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8182 (p) REVERT: B 531 GLN cc_start: 0.8604 (tt0) cc_final: 0.8239 (tt0) outliers start: 36 outliers final: 8 residues processed: 156 average time/residue: 0.7060 time to fit residues: 115.8720 Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 319 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.087096 restraints weight = 11139.598| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.42 r_work: 0.2787 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8648 Z= 0.157 Angle : 0.678 10.057 11842 Z= 0.311 Chirality : 0.044 0.180 1466 Planarity : 0.004 0.039 1404 Dihedral : 10.392 134.705 1648 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.31 % Allowed : 12.02 % Favored : 83.67 % 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: 0.77 (0.26), residues: 1070 helix: 1.61 (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 0.006 0.000 ARG B 528 TYR 0.015 0.001 TYR A 651 PHE 0.014 0.002 PHE B 258 TRP 0.010 0.001 TRP A 381 HIS 0.002 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8626) covalent geometry : angle 0.62600 (11794) SS BOND : bond 0.00323 ( 6) SS BOND : angle 1.47009 ( 12) hydrogen bonds : bond 0.04361 ( 494) hydrogen bonds : angle 3.83174 ( 1434) Misc. bond : bond 0.00028 ( 4) link_ALPHA1-4 : bond 0.01379 ( 4) link_ALPHA1-4 : angle 2.34060 ( 12) link_BETA1-4 : bond 0.00978 ( 4) link_BETA1-4 : angle 5.89520 ( 12) link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 5.06354 ( 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 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.302 Fit side-chains REVERT: A 179 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 190 SER cc_start: 0.8935 (t) cc_final: 0.8330 (p) REVERT: A 275 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7970 (ttmm) REVERT: A 378 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: A 405 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8463 (ttpp) REVERT: A 566 GLU cc_start: 0.9386 (tp30) cc_final: 0.9160 (tp30) REVERT: B 122 MET cc_start: 0.8922 (tpp) cc_final: 0.8629 (mmm) REVERT: B 179 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8194 (p) REVERT: B 378 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: B 386 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7898 (tp30) outliers start: 38 outliers final: 8 residues processed: 153 average time/residue: 0.7138 time to fit residues: 114.9160 Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU 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 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: 0.6980 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 319 GLN A 439 ASN A 531 GLN A 537 ASN B 319 GLN B 551 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.087333 restraints weight = 11092.075| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.43 r_work: 0.2783 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3005 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= 0.161 Angle : 1.042 59.199 11842 Z= 0.529 Chirality : 0.046 0.361 1466 Planarity : 0.004 0.038 1404 Dihedral : 10.475 134.119 1648 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.85 % Allowed : 13.72 % Favored : 82.43 % 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: 1.75 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.011 0.001 TYR B 411 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8626) covalent geometry : angle 1.00043 (11794) SS BOND : bond 0.00375 ( 6) SS BOND : angle 1.38641 ( 12) hydrogen bonds : bond 0.04246 ( 494) hydrogen bonds : angle 3.82975 ( 1434) Misc. bond : bond 0.00025 ( 4) link_ALPHA1-4 : bond 0.01308 ( 4) link_ALPHA1-4 : angle 2.32206 ( 12) link_BETA1-4 : bond 0.01577 ( 4) link_BETA1-4 : angle 6.93438 ( 12) link_NAG-ASN : bond 0.04009 ( 4) link_NAG-ASN : angle 5.63560 ( 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 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 190 SER cc_start: 0.8962 (t) cc_final: 0.8346 (p) REVERT: A 275 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7984 (ttmm) REVERT: A 378 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: A 405 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8470 (ttpp) REVERT: A 566 GLU cc_start: 0.9379 (tp30) cc_final: 0.9136 (tp30) REVERT: B 122 MET cc_start: 0.8894 (tpp) cc_final: 0.8577 (mmm) REVERT: B 179 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 377 GLN cc_start: 0.8132 (tp40) cc_final: 0.7604 (mm110) REVERT: B 378 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: B 480 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8544 (m) outliers start: 34 outliers final: 17 residues processed: 140 average time/residue: 0.7208 time to fit residues: 105.9025 Evaluate side-chains 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 610 ARG 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 359 LEU 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 480 VAL 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: 0.6980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN 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 = 0.3389 r_free = 0.3389 target = 0.118227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087215 restraints weight = 10979.003| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.42 r_work: 0.2791 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3009 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= 0.161 Angle : 1.042 59.199 11842 Z= 0.529 Chirality : 0.046 0.361 1466 Planarity : 0.004 0.038 1404 Dihedral : 10.475 134.119 1648 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 15.08 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.011 0.001 TYR B 411 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8626) covalent geometry : angle 1.00043 (11794) SS BOND : bond 0.00375 ( 6) SS BOND : angle 1.38641 ( 12) hydrogen bonds : bond 0.04246 ( 494) hydrogen bonds : angle 3.82975 ( 1434) Misc. bond : bond 0.00025 ( 4) link_ALPHA1-4 : bond 0.01308 ( 4) link_ALPHA1-4 : angle 2.32206 ( 12) link_BETA1-4 : bond 0.01577 ( 4) link_BETA1-4 : angle 6.93438 ( 12) link_NAG-ASN : bond 0.04009 ( 4) link_NAG-ASN : angle 5.63560 ( 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 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 190 SER cc_start: 0.8962 (t) cc_final: 0.8347 (p) REVERT: A 275 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7983 (ttmm) REVERT: A 378 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: A 405 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: A 566 GLU cc_start: 0.9375 (tp30) cc_final: 0.9128 (tp30) REVERT: B 122 MET cc_start: 0.8870 (tpp) cc_final: 0.8573 (mmm) REVERT: B 179 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 377 GLN cc_start: 0.8125 (tp40) cc_final: 0.7597 (mm110) REVERT: B 378 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (mt-10) REVERT: B 480 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8550 (m) outliers start: 25 outliers final: 17 residues processed: 137 average time/residue: 0.7717 time to fit residues: 110.8593 Evaluate side-chains 148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 610 ARG 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 359 LEU 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 480 VAL 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: 0.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN 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 = 0.3390 r_free = 0.3390 target = 0.118273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.087152 restraints weight = 11081.868| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.44 r_work: 0.2708 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3005 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= 0.161 Angle : 1.041 59.169 11842 Z= 0.529 Chirality : 0.046 0.361 1466 Planarity : 0.004 0.038 1404 Dihedral : 10.475 134.119 1648 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 15.08 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.011 0.001 TYR B 411 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8626) covalent geometry : angle 1.00016 (11794) SS BOND : bond 0.00377 ( 6) SS BOND : angle 1.38650 ( 12) hydrogen bonds : bond 0.04245 ( 494) hydrogen bonds : angle 3.82973 ( 1434) Misc. bond : bond 0.00025 ( 4) link_ALPHA1-4 : bond 0.01307 ( 4) link_ALPHA1-4 : angle 2.31982 ( 12) link_BETA1-4 : bond 0.01578 ( 4) link_BETA1-4 : angle 6.93289 ( 12) link_NAG-ASN : bond 0.04002 ( 4) link_NAG-ASN : angle 5.63585 ( 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 148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 190 SER cc_start: 0.8927 (t) cc_final: 0.8290 (p) REVERT: A 275 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7951 (ttmm) REVERT: A 378 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: A 405 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8396 (ttpp) REVERT: A 566 GLU cc_start: 0.9363 (tp30) cc_final: 0.9114 (tp30) REVERT: B 122 MET cc_start: 0.8846 (tpp) cc_final: 0.8543 (mmm) REVERT: B 179 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 377 GLN cc_start: 0.8053 (tp40) cc_final: 0.7516 (mm110) REVERT: B 378 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: B 480 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8452 (m) outliers start: 25 outliers final: 16 residues processed: 136 average time/residue: 0.7645 time to fit residues: 109.0584 Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 610 ARG 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 359 LEU 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 480 VAL 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: 0.2980 chunk 70 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN 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 = 0.3389 r_free = 0.3389 target = 0.118245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087248 restraints weight = 10963.357| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.42 r_work: 0.2793 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3007 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= 0.161 Angle : 1.041 59.169 11842 Z= 0.529 Chirality : 0.046 0.361 1466 Planarity : 0.004 0.038 1404 Dihedral : 10.475 134.119 1648 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.72 % Allowed : 15.19 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.011 0.001 TYR B 411 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8626) covalent geometry : angle 1.00016 (11794) SS BOND : bond 0.00377 ( 6) SS BOND : angle 1.38650 ( 12) hydrogen bonds : bond 0.04245 ( 494) hydrogen bonds : angle 3.82973 ( 1434) Misc. bond : bond 0.00025 ( 4) link_ALPHA1-4 : bond 0.01307 ( 4) link_ALPHA1-4 : angle 2.31982 ( 12) link_BETA1-4 : bond 0.01578 ( 4) link_BETA1-4 : angle 6.93288 ( 12) link_NAG-ASN : bond 0.04002 ( 4) link_NAG-ASN : angle 5.63585 ( 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 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 190 SER cc_start: 0.8962 (t) cc_final: 0.8348 (p) REVERT: A 275 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7983 (ttmm) REVERT: A 378 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: A 405 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: A 566 GLU cc_start: 0.9376 (tp30) cc_final: 0.9128 (tp30) REVERT: B 122 MET cc_start: 0.8874 (tpp) cc_final: 0.8576 (mmm) REVERT: B 179 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 377 GLN cc_start: 0.8124 (tp40) cc_final: 0.7596 (mm110) REVERT: B 378 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8556 (mt-10) REVERT: B 480 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8548 (m) outliers start: 24 outliers final: 16 residues processed: 136 average time/residue: 0.7837 time to fit residues: 111.6144 Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 610 ARG 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 359 LEU 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 480 VAL 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: 0.6980 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN 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 = 0.3389 r_free = 0.3389 target = 0.118246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.087236 restraints weight = 10985.194| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.42 r_work: 0.2792 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3007 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= 0.161 Angle : 1.041 59.163 11842 Z= 0.529 Chirality : 0.046 0.361 1466 Planarity : 0.004 0.038 1404 Dihedral : 10.475 134.119 1648 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.72 % Allowed : 15.19 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.011 0.001 TYR B 411 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8626) covalent geometry : angle 1.00011 (11794) SS BOND : bond 0.00378 ( 6) SS BOND : angle 1.38651 ( 12) hydrogen bonds : bond 0.04245 ( 494) hydrogen bonds : angle 3.82973 ( 1434) Misc. bond : bond 0.00025 ( 4) link_ALPHA1-4 : bond 0.01307 ( 4) link_ALPHA1-4 : angle 2.31955 ( 12) link_BETA1-4 : bond 0.01578 ( 4) link_BETA1-4 : angle 6.93263 ( 12) link_NAG-ASN : bond 0.04000 ( 4) link_NAG-ASN : angle 5.63592 ( 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 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 190 SER cc_start: 0.8963 (t) cc_final: 0.8348 (p) REVERT: A 275 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7983 (ttmm) REVERT: A 378 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: A 405 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: A 566 GLU cc_start: 0.9376 (tp30) cc_final: 0.9128 (tp30) REVERT: B 122 MET cc_start: 0.8873 (tpp) cc_final: 0.8576 (mmm) REVERT: B 179 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 377 GLN cc_start: 0.8124 (tp40) cc_final: 0.7597 (mm110) REVERT: B 378 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: B 480 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8547 (m) outliers start: 24 outliers final: 16 residues processed: 136 average time/residue: 0.8074 time to fit residues: 114.9867 Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 610 ARG 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 359 LEU 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 480 VAL 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: 0.9990 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN 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 = 0.3389 r_free = 0.3389 target = 0.118201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.087177 restraints weight = 11036.410| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.43 r_work: 0.2792 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8648 Z= 0.172 Angle : 1.014 59.185 11842 Z= 0.525 Chirality : 0.047 0.473 1466 Planarity : 0.004 0.046 1404 Dihedral : 10.460 134.039 1648 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.29 % Allowed : 14.74 % 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: 0.95 (0.26), residues: 1070 helix: 1.77 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 191 TYR 0.026 0.001 TYR A 613 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8626) covalent geometry : angle 0.97377 (11794) SS BOND : bond 0.00718 ( 6) SS BOND : angle 1.56377 ( 12) hydrogen bonds : bond 0.04242 ( 494) hydrogen bonds : angle 3.82647 ( 1434) Misc. bond : bond 0.00026 ( 4) link_ALPHA1-4 : bond 0.01313 ( 4) link_ALPHA1-4 : angle 2.28527 ( 12) link_BETA1-4 : bond 0.01134 ( 4) link_BETA1-4 : angle 6.48916 ( 12) link_NAG-ASN : bond 0.03302 ( 4) link_NAG-ASN : angle 5.73826 ( 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 152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 179 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8172 (p) REVERT: A 190 SER cc_start: 0.8950 (t) cc_final: 0.8337 (p) REVERT: A 275 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7983 (ttmm) REVERT: A 378 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8656 (mt-10) REVERT: A 405 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: A 566 GLU cc_start: 0.9376 (tp30) cc_final: 0.9130 (tp30) REVERT: B 122 MET cc_start: 0.8868 (tpp) cc_final: 0.8573 (mmm) REVERT: B 179 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8187 (p) REVERT: B 377 GLN cc_start: 0.8124 (tp40) cc_final: 0.7596 (mm110) REVERT: B 378 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: B 480 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8544 (m) outliers start: 29 outliers final: 16 residues processed: 137 average time/residue: 0.7586 time to fit residues: 108.8729 Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 610 ARG 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 359 LEU 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 480 VAL 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: 3.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 531 GLN A 537 ASN B 319 GLN B 537 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 = 0.3389 r_free = 0.3389 target = 0.118220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.087168 restraints weight = 10992.926| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.42 r_work: 0.2705 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8648 Z= 0.170 Angle : 1.012 58.833 11842 Z= 0.524 Chirality : 0.047 0.449 1466 Planarity : 0.004 0.046 1404 Dihedral : 10.468 134.038 1648 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.83 % Allowed : 15.19 % 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: 0.95 (0.26), residues: 1070 helix: 1.77 (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 0.013 0.001 ARG B 191 TYR 0.025 0.001 TYR A 613 PHE 0.010 0.001 PHE B 428 TRP 0.008 0.001 TRP A 381 HIS 0.001 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8626) covalent geometry : angle 0.97168 (11794) SS BOND : bond 0.00701 ( 6) SS BOND : angle 1.57412 ( 12) hydrogen bonds : bond 0.04251 ( 494) hydrogen bonds : angle 3.82606 ( 1434) Misc. bond : bond 0.00027 ( 4) link_ALPHA1-4 : bond 0.01420 ( 4) link_ALPHA1-4 : angle 2.34294 ( 12) link_BETA1-4 : bond 0.01150 ( 4) link_BETA1-4 : angle 6.48024 ( 12) link_NAG-ASN : bond 0.03293 ( 4) link_NAG-ASN : angle 5.69387 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.49 seconds wall clock time: 53 minutes 56.50 seconds (3236.50 seconds total)