Starting phenix.real_space_refine on Sat Aug 23 13:16:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lw1_30002/08_2025/6lw1_30002.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lw1_30002/08_2025/6lw1_30002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lw1_30002/08_2025/6lw1_30002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lw1_30002/08_2025/6lw1_30002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lw1_30002/08_2025/6lw1_30002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lw1_30002/08_2025/6lw1_30002.map" } resolution = 2.8 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= 0.007 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 7956 2.51 5 N 2116 2.21 5 O 2278 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6170 Classifications: {'peptide': 763} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 727} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'EX3': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 4.41, per 1000 atoms: 0.36 Number of scatterers: 12412 At special positions: 0 Unit cell: (100.596, 128.484, 105.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 2 9.00 O 2278 8.00 N 2116 7.00 C 7956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 475 " distance=2.02 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.02 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.04 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 475 " distance=2.02 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.02 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.04 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 833 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 355.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 14.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.914A pdb=" N ALA A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 4.001A pdb=" N ASN A 276 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.561A pdb=" N ASP A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.531A pdb=" N PHE A 338 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.526A pdb=" N PHE A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 369 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.556A pdb=" N LEU A 390 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 391 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Proline residue: A 392 - end of helix removed outlier: 4.138A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 396' Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.810A pdb=" N GLN A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 576 through 582 removed outlier: 4.287A pdb=" N PHE A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.895A pdb=" N LEU A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 removed outlier: 3.540A pdb=" N MET A 673 " --> pdb=" O PHE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 698 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.535A pdb=" N SER A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 799 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.569A pdb=" N HIS A 820 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 4.043A pdb=" N GLU A 834 " --> pdb=" O TYR A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.914A pdb=" N ALA B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 removed outlier: 4.000A pdb=" N ASN B 276 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.560A pdb=" N ASP B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.532A pdb=" N PHE B 338 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.525A pdb=" N PHE B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 369 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.556A pdb=" N LEU B 390 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 391 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 392 - end of helix removed outlier: 4.138A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 396 " --> pdb=" O LEU B 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 396' Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.809A pdb=" N GLN B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 576 through 582 removed outlier: 4.287A pdb=" N PHE B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 582 " --> pdb=" O HIS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.894A pdb=" N LEU B 634 " --> pdb=" O HIS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.541A pdb=" N MET B 673 " --> pdb=" O PHE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 698 Processing helix chain 'B' and resid 717 through 722 removed outlier: 3.536A pdb=" N SER B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 791 through 799 Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.569A pdb=" N HIS B 820 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 4.043A pdb=" N GLU B 834 " --> pdb=" O TYR B 831 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.597A pdb=" N ASP A 37 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 69 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 94 " --> pdb=" O TYR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 removed outlier: 7.089A pdb=" N LEU A 153 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 177 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 230 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 254 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 319 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 403 removed outlier: 6.609A pdb=" N LEU A 402 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 426 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 498 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 522 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 547 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 571 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 601 " --> pdb=" O GLU A 625 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 532 removed outlier: 6.626A pdb=" N GLN A 531 " --> pdb=" O ASP A 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 752 through 753 removed outlier: 7.205A pdb=" N LEU A 752 " --> pdb=" O LEU A 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 813 through 814 removed outlier: 3.965A pdb=" N GLN A 823 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.597A pdb=" N ASP B 37 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 69 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE B 94 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 154 removed outlier: 7.089A pdb=" N LEU B 153 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 177 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 230 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 254 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 319 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AB3, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.610A pdb=" N LEU B 402 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE B 426 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 498 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 522 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 547 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 571 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 601 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 530 through 532 removed outlier: 6.627A pdb=" N GLN B 531 " --> pdb=" O ASP B 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 752 through 753 removed outlier: 7.204A pdb=" N LEU B 752 " --> pdb=" O LEU B 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 813 through 814 removed outlier: 3.966A pdb=" N GLN B 823 " --> pdb=" O CYS B 814 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 174 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: 1.95 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3741 1.33 - 1.46: 2544 1.46 - 1.58: 6311 1.58 - 1.70: 0 1.70 - 1.83: 82 Bond restraints: 12678 Sorted by residual: bond pdb=" C20 EX3 A1001 " pdb=" C22 EX3 A1001 " ideal model delta sigma weight residual 1.536 1.456 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C22 EX3 A1001 " pdb=" C25 EX3 A1001 " ideal model delta sigma weight residual 1.526 1.446 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C22 EX3 B1001 " pdb=" C25 EX3 B1001 " ideal model delta sigma weight residual 1.526 1.446 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C20 EX3 B1001 " pdb=" C22 EX3 B1001 " ideal model delta sigma weight residual 1.536 1.457 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C EX3 A1001 " pdb=" C2 EX3 A1001 " ideal model delta sigma weight residual 1.395 1.459 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 12673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 17074 3.61 - 7.22: 96 7.22 - 10.84: 6 10.84 - 14.45: 2 14.45 - 18.06: 10 Bond angle restraints: 17188 Sorted by residual: angle pdb=" C22 EX3 A1001 " pdb=" N6 EX3 A1001 " pdb=" C23 EX3 A1001 " ideal model delta sigma weight residual 105.46 87.40 18.06 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C22 EX3 B1001 " pdb=" N6 EX3 B1001 " pdb=" C23 EX3 B1001 " ideal model delta sigma weight residual 105.46 87.45 18.01 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C22 EX3 A1001 " pdb=" C20 EX3 A1001 " pdb=" N5 EX3 A1001 " ideal model delta sigma weight residual 102.54 85.93 16.61 3.00e+00 1.11e-01 3.07e+01 angle pdb=" C22 EX3 B1001 " pdb=" C20 EX3 B1001 " pdb=" N5 EX3 B1001 " ideal model delta sigma weight residual 102.54 85.95 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" C21 EX3 A1001 " pdb=" C25 EX3 A1001 " pdb=" C22 EX3 A1001 " ideal model delta sigma weight residual 91.43 75.22 16.21 3.00e+00 1.11e-01 2.92e+01 ... (remaining 17183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6666 17.91 - 35.81: 858 35.81 - 53.72: 202 53.72 - 71.62: 68 71.62 - 89.53: 12 Dihedral angle restraints: 7806 sinusoidal: 3278 harmonic: 4528 Sorted by residual: dihedral pdb=" CB CYS B 263 " pdb=" SG CYS B 263 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 -177.47 -89.53 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual 93.00 -177.48 -89.52 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CA SER B 429 " pdb=" C SER B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta harmonic sigma weight residual -180.00 -140.70 -39.30 0 5.00e+00 4.00e-02 6.18e+01 ... (remaining 7803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.389: 1968 0.389 - 0.779: 0 0.779 - 1.168: 0 1.168 - 1.557: 0 1.557 - 1.946: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" C22 EX3 A1001 " pdb=" C20 EX3 A1001 " pdb=" C25 EX3 A1001 " pdb=" N6 EX3 A1001 " both_signs ideal model delta sigma weight residual False 3.01 1.07 1.95 2.00e-01 2.50e+01 9.47e+01 chirality pdb=" C22 EX3 B1001 " pdb=" C20 EX3 B1001 " pdb=" C25 EX3 B1001 " pdb=" N6 EX3 B1001 " both_signs ideal model delta sigma weight residual False 3.01 1.07 1.94 2.00e-01 2.50e+01 9.43e+01 chirality pdb=" CB VAL A 381 " pdb=" CA VAL A 381 " pdb=" CG1 VAL A 381 " pdb=" CG2 VAL A 381 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1967 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N EX3 B1001 " -0.001 2.00e-02 2.50e+03 1.28e-02 5.30e+00 pdb=" C EX3 B1001 " 0.001 2.00e-02 2.50e+03 pdb=" O EX3 B1001 " -0.001 2.00e-02 2.50e+03 pdb=" C1 EX3 B1001 " 0.007 2.00e-02 2.50e+03 pdb=" C14 EX3 B1001 " -0.030 2.00e-02 2.50e+03 pdb=" C2 EX3 B1001 " -0.002 2.00e-02 2.50e+03 pdb=" C26 EX3 B1001 " -0.000 2.00e-02 2.50e+03 pdb=" C3 EX3 B1001 " -0.005 2.00e-02 2.50e+03 pdb=" C4 EX3 B1001 " 0.033 2.00e-02 2.50e+03 pdb=" C7 EX3 B1001 " -0.003 2.00e-02 2.50e+03 pdb=" N1 EX3 B1001 " -0.006 2.00e-02 2.50e+03 pdb=" N2 EX3 B1001 " 0.004 2.00e-02 2.50e+03 pdb=" N3 EX3 B1001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N EX3 A1001 " 0.001 2.00e-02 2.50e+03 1.27e-02 5.21e+00 pdb=" C EX3 A1001 " -0.001 2.00e-02 2.50e+03 pdb=" O EX3 A1001 " 0.001 2.00e-02 2.50e+03 pdb=" C1 EX3 A1001 " -0.006 2.00e-02 2.50e+03 pdb=" C14 EX3 A1001 " 0.030 2.00e-02 2.50e+03 pdb=" C2 EX3 A1001 " 0.002 2.00e-02 2.50e+03 pdb=" C26 EX3 A1001 " 0.000 2.00e-02 2.50e+03 pdb=" C3 EX3 A1001 " 0.005 2.00e-02 2.50e+03 pdb=" C4 EX3 A1001 " -0.032 2.00e-02 2.50e+03 pdb=" C7 EX3 A1001 " 0.003 2.00e-02 2.50e+03 pdb=" N1 EX3 A1001 " 0.006 2.00e-02 2.50e+03 pdb=" N2 EX3 A1001 " -0.004 2.00e-02 2.50e+03 pdb=" N3 EX3 A1001 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 434 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 435 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 435 " 0.025 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 325 2.67 - 3.23: 11920 3.23 - 3.79: 18818 3.79 - 4.34: 28604 4.34 - 4.90: 45417 Nonbonded interactions: 105084 Sorted by model distance: nonbonded pdb=" O SER A 429 " pdb=" N ASN A 431 " model vdw 2.119 3.120 nonbonded pdb=" O SER B 429 " pdb=" N ASN B 431 " model vdw 2.119 3.120 nonbonded pdb=" O SER A 429 " pdb=" ND2 ASN A 431 " model vdw 2.161 3.120 nonbonded pdb=" O SER B 429 " pdb=" ND2 ASN B 431 " model vdw 2.161 3.120 nonbonded pdb=" O SER A 504 " pdb=" OG SER A 504 " model vdw 2.163 3.040 ... (remaining 105079 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' } 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: 0.930 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.009 0.080 12694 Z= 0.381 Angle : 0.909 18.060 17220 Z= 0.451 Chirality : 0.080 1.946 1970 Planarity : 0.004 0.045 2180 Dihedral : 17.419 86.664 4798 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.30 % Favored : 89.17 % Rotamer: Outliers : 7.10 % Allowed : 24.30 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 aren not related in a simple way. whole: -3.85 (0.19), residues: 1514 helix: -4.31 (0.27), residues: 116 sheet: -3.65 (0.28), residues: 268 loop : -2.22 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.020 0.002 TYR B 233 PHE 0.016 0.002 PHE A 96 TRP 0.009 0.001 TRP B 793 HIS 0.006 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00886 (12678) covalent geometry : angle 0.90810 (17188) SS BOND : bond 0.00674 ( 16) SS BOND : angle 1.42401 ( 32) hydrogen bonds : bond 0.29303 ( 88) hydrogen bonds : angle 8.27823 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 143 time to evaluate : 0.409 Fit side-chains REVERT: A 95 ASP cc_start: 0.7113 (t0) cc_final: 0.6855 (t0) REVERT: A 135 ASP cc_start: 0.7711 (m-30) cc_final: 0.7409 (m-30) REVERT: A 167 GLN cc_start: 0.7474 (pt0) cc_final: 0.7105 (pt0) REVERT: A 360 MET cc_start: 0.8385 (ttp) cc_final: 0.8173 (ttp) REVERT: A 514 GLN cc_start: 0.7736 (tt0) cc_final: 0.7469 (mt0) REVERT: A 723 ARG cc_start: 0.7154 (tpt90) cc_final: 0.6818 (mmm160) REVERT: A 759 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4429 (tp) REVERT: A 829 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3378 (t70) REVERT: B 130 LYS cc_start: 0.7276 (mttt) cc_final: 0.7034 (mmtp) REVERT: B 135 ASP cc_start: 0.7676 (m-30) cc_final: 0.7409 (m-30) REVERT: B 207 LYS cc_start: 0.8223 (mttm) cc_final: 0.7556 (mtmt) REVERT: B 360 MET cc_start: 0.8385 (ttp) cc_final: 0.8170 (ttp) REVERT: B 514 GLN cc_start: 0.7713 (tt0) cc_final: 0.7426 (mt0) REVERT: B 673 MET cc_start: 0.8356 (mmt) cc_final: 0.7706 (mtp) REVERT: B 697 TYR cc_start: 0.7550 (m-10) cc_final: 0.7244 (m-10) REVERT: B 710 GLN cc_start: 0.7603 (mp10) cc_final: 0.7364 (mp10) REVERT: B 759 ILE cc_start: 0.5006 (OUTLIER) cc_final: 0.4389 (tp) REVERT: B 829 ASP cc_start: 0.3755 (OUTLIER) cc_final: 0.3204 (t70) outliers start: 102 outliers final: 47 residues processed: 233 average time/residue: 0.3252 time to fit residues: 85.3953 Evaluate side-chains 174 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 THR Chi-restraints excluded: chain B residue 766 SER Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 30.0000 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 75 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 159 ASN A 167 GLN A 181 GLN A 252 GLN A 276 ASN A 280 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN A 389 GLN A 407 ASN A 503 ASN A 720 ASN A 727 ASN A 732 ASN A 744 GLN A 781 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 159 ASN B 167 GLN B 181 GLN B 252 GLN B 276 ASN B 280 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 GLN B 407 ASN B 503 ASN B 720 ASN B 727 ASN B 732 ASN B 744 GLN B 781 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.214896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141404 restraints weight = 12284.671| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.77 r_work: 0.3536 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12694 Z= 0.127 Angle : 0.610 8.991 17220 Z= 0.310 Chirality : 0.045 0.141 1970 Planarity : 0.004 0.033 2180 Dihedral : 7.834 57.841 1766 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 5.36 % Allowed : 23.33 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -2.87 (0.21), residues: 1514 helix: -3.89 (0.29), residues: 114 sheet: -3.24 (0.31), residues: 268 loop : -1.40 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.011 0.001 TYR A 233 PHE 0.015 0.001 PHE B 664 TRP 0.011 0.001 TRP B 793 HIS 0.003 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00290 (12678) covalent geometry : angle 0.60971 (17188) SS BOND : bond 0.00503 ( 16) SS BOND : angle 0.66262 ( 32) hydrogen bonds : bond 0.04137 ( 88) hydrogen bonds : angle 6.25182 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 130 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.4161 (pmt170) REVERT: A 130 LYS cc_start: 0.7097 (mttt) cc_final: 0.6887 (mmtp) REVERT: A 207 LYS cc_start: 0.7918 (mttm) cc_final: 0.7156 (mtmt) REVERT: A 509 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7667 (tttm) REVERT: A 510 SER cc_start: 0.8536 (p) cc_final: 0.8282 (t) REVERT: A 514 GLN cc_start: 0.7962 (tt0) cc_final: 0.7544 (mt0) REVERT: A 653 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 697 TYR cc_start: 0.7638 (m-10) cc_final: 0.7251 (m-80) REVERT: A 710 GLN cc_start: 0.7558 (mp10) cc_final: 0.7178 (mp10) REVERT: A 723 ARG cc_start: 0.7201 (tpt90) cc_final: 0.6852 (mmm160) REVERT: A 734 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: A 759 ILE cc_start: 0.4780 (OUTLIER) cc_final: 0.4175 (tp) REVERT: A 782 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.5479 (m170) REVERT: A 829 ASP cc_start: 0.3428 (OUTLIER) cc_final: 0.2816 (t70) REVERT: B 87 ARG cc_start: 0.4387 (OUTLIER) cc_final: 0.4109 (pmt170) REVERT: B 95 ASP cc_start: 0.7480 (t0) cc_final: 0.7055 (t70) REVERT: B 130 LYS cc_start: 0.7174 (mttt) cc_final: 0.6953 (mmtp) REVERT: B 207 LYS cc_start: 0.8007 (mttm) cc_final: 0.7219 (mtmt) REVERT: B 509 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7644 (tttm) REVERT: B 514 GLN cc_start: 0.7937 (tt0) cc_final: 0.7470 (mt0) REVERT: B 653 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 697 TYR cc_start: 0.7687 (m-10) cc_final: 0.7380 (m-80) REVERT: B 710 GLN cc_start: 0.7589 (mp10) cc_final: 0.7356 (mp10) REVERT: B 734 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 759 ILE cc_start: 0.4764 (OUTLIER) cc_final: 0.4144 (tp) REVERT: B 782 HIS cc_start: 0.6090 (OUTLIER) cc_final: 0.5490 (m170) REVERT: B 829 ASP cc_start: 0.3512 (OUTLIER) cc_final: 0.2883 (t70) outliers start: 77 outliers final: 28 residues processed: 198 average time/residue: 0.3385 time to fit residues: 75.6809 Evaluate side-chains 157 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 734 GLN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 782 HIS Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141880 restraints weight = 12326.712| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.80 r_work: 0.3538 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12694 Z= 0.118 Angle : 0.565 9.167 17220 Z= 0.289 Chirality : 0.044 0.171 1970 Planarity : 0.003 0.032 2180 Dihedral : 6.173 55.712 1723 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.74 % Favored : 93.00 % Rotamer: Outliers : 5.01 % Allowed : 24.44 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -2.49 (0.22), residues: 1514 helix: -3.67 (0.31), residues: 114 sheet: -3.07 (0.31), residues: 272 loop : -1.08 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.014 0.001 TYR A 233 PHE 0.011 0.001 PHE B 664 TRP 0.011 0.001 TRP B 793 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00271 (12678) covalent geometry : angle 0.56454 (17188) SS BOND : bond 0.00255 ( 16) SS BOND : angle 0.75839 ( 32) hydrogen bonds : bond 0.03394 ( 88) hydrogen bonds : angle 5.66365 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 124 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7196 (mttt) cc_final: 0.6868 (mtpp) REVERT: A 207 LYS cc_start: 0.7896 (mttm) cc_final: 0.7132 (mtmt) REVERT: A 509 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7634 (tttm) REVERT: A 510 SER cc_start: 0.8540 (p) cc_final: 0.8324 (t) REVERT: A 514 GLN cc_start: 0.7966 (tt0) cc_final: 0.7546 (mt0) REVERT: A 653 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 697 TYR cc_start: 0.7628 (m-10) cc_final: 0.7358 (m-80) REVERT: A 710 GLN cc_start: 0.7564 (mp10) cc_final: 0.7169 (mp10) REVERT: A 723 ARG cc_start: 0.7290 (tpt90) cc_final: 0.6893 (mmm160) REVERT: A 734 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6850 (mp10) REVERT: A 759 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4142 (tp) REVERT: A 829 ASP cc_start: 0.3446 (OUTLIER) cc_final: 0.2826 (t70) REVERT: B 87 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.4195 (pmt170) REVERT: B 130 LYS cc_start: 0.7212 (mttt) cc_final: 0.7012 (mmtp) REVERT: B 207 LYS cc_start: 0.7976 (mttm) cc_final: 0.7198 (mtmt) REVERT: B 246 ASN cc_start: 0.8207 (t0) cc_final: 0.8006 (t0) REVERT: B 509 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7649 (tttm) REVERT: B 514 GLN cc_start: 0.7937 (tt0) cc_final: 0.7515 (mt0) REVERT: B 653 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 697 TYR cc_start: 0.7710 (m-10) cc_final: 0.7415 (m-80) REVERT: B 723 ARG cc_start: 0.7389 (tpt90) cc_final: 0.6926 (mmm160) REVERT: B 727 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6754 (m-40) REVERT: B 759 ILE cc_start: 0.4780 (OUTLIER) cc_final: 0.4170 (tp) REVERT: B 781 HIS cc_start: 0.5381 (p90) cc_final: 0.5108 (p90) REVERT: B 829 ASP cc_start: 0.3574 (OUTLIER) cc_final: 0.2997 (t70) outliers start: 72 outliers final: 28 residues processed: 186 average time/residue: 0.3901 time to fit residues: 81.5457 Evaluate side-chains 153 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 130 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 117 GLN A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.215539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141549 restraints weight = 12349.247| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.80 r_work: 0.3528 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12694 Z= 0.133 Angle : 0.553 8.756 17220 Z= 0.283 Chirality : 0.045 0.200 1970 Planarity : 0.003 0.033 2180 Dihedral : 6.013 55.843 1721 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.61 % Favored : 93.00 % Rotamer: Outliers : 4.74 % Allowed : 24.23 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -2.26 (0.22), residues: 1514 helix: -3.38 (0.34), residues: 114 sheet: -2.87 (0.32), residues: 272 loop : -0.94 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.014 0.001 TYR A 233 PHE 0.010 0.001 PHE B 507 TRP 0.010 0.001 TRP B 793 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00309 (12678) covalent geometry : angle 0.55275 (17188) SS BOND : bond 0.00660 ( 16) SS BOND : angle 0.69198 ( 32) hydrogen bonds : bond 0.03010 ( 88) hydrogen bonds : angle 5.38937 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 119 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7171 (mttt) cc_final: 0.6832 (mtpp) REVERT: A 207 LYS cc_start: 0.7917 (mttm) cc_final: 0.7164 (mtmt) REVERT: A 509 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7658 (tttm) REVERT: A 510 SER cc_start: 0.8529 (p) cc_final: 0.8324 (t) REVERT: A 514 GLN cc_start: 0.7959 (tt0) cc_final: 0.7542 (mt0) REVERT: A 653 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 697 TYR cc_start: 0.7656 (m-10) cc_final: 0.7382 (m-80) REVERT: A 710 GLN cc_start: 0.7672 (mp10) cc_final: 0.7338 (mp10) REVERT: A 723 ARG cc_start: 0.7245 (tpt90) cc_final: 0.6822 (mmm160) REVERT: A 734 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: A 759 ILE cc_start: 0.4768 (OUTLIER) cc_final: 0.4399 (tp) REVERT: A 829 ASP cc_start: 0.3407 (OUTLIER) cc_final: 0.2855 (t70) REVERT: B 87 ARG cc_start: 0.4468 (OUTLIER) cc_final: 0.4195 (pmt170) REVERT: B 130 LYS cc_start: 0.7219 (mttt) cc_final: 0.6912 (mtpp) REVERT: B 196 GLU cc_start: 0.7943 (pt0) cc_final: 0.7658 (pt0) REVERT: B 207 LYS cc_start: 0.7992 (mttm) cc_final: 0.7206 (mtmt) REVERT: B 509 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7666 (tttm) REVERT: B 514 GLN cc_start: 0.7985 (tt0) cc_final: 0.7544 (mt0) REVERT: B 602 MET cc_start: 0.8918 (mtm) cc_final: 0.8600 (mpp) REVERT: B 653 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 697 TYR cc_start: 0.7736 (m-10) cc_final: 0.7418 (m-10) REVERT: B 739 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6801 (p) REVERT: B 759 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4089 (tp) REVERT: B 829 ASP cc_start: 0.3443 (OUTLIER) cc_final: 0.2841 (t70) outliers start: 68 outliers final: 25 residues processed: 181 average time/residue: 0.3469 time to fit residues: 70.9758 Evaluate side-chains 147 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 106 optimal weight: 0.0770 chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 0.0010 chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 732 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.216609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142815 restraints weight = 12350.333| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.81 r_work: 0.3542 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12694 Z= 0.109 Angle : 0.532 8.505 17220 Z= 0.275 Chirality : 0.044 0.192 1970 Planarity : 0.003 0.033 2180 Dihedral : 5.819 55.857 1720 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 3.90 % Allowed : 25.00 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: -2.24 (0.22), residues: 1514 helix: -3.29 (0.32), residues: 138 sheet: -2.77 (0.32), residues: 272 loop : -0.89 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 473 TYR 0.013 0.001 TYR B 546 PHE 0.011 0.001 PHE B 507 TRP 0.010 0.001 TRP B 793 HIS 0.003 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00252 (12678) covalent geometry : angle 0.53061 (17188) SS BOND : bond 0.00463 ( 16) SS BOND : angle 0.93606 ( 32) hydrogen bonds : bond 0.02752 ( 88) hydrogen bonds : angle 5.17406 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7147 (mttt) cc_final: 0.6878 (mmtp) REVERT: A 207 LYS cc_start: 0.7876 (mttm) cc_final: 0.7110 (mtmt) REVERT: A 509 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7639 (tttm) REVERT: A 514 GLN cc_start: 0.7937 (tt0) cc_final: 0.7508 (mt0) REVERT: A 636 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5553 (ttp-170) REVERT: A 653 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 697 TYR cc_start: 0.7660 (m-10) cc_final: 0.7407 (m-80) REVERT: A 710 GLN cc_start: 0.7681 (mp10) cc_final: 0.7392 (mp10) REVERT: A 723 ARG cc_start: 0.7236 (tpt90) cc_final: 0.6877 (mmm160) REVERT: A 738 LEU cc_start: 0.7253 (mp) cc_final: 0.6893 (tp) REVERT: A 759 ILE cc_start: 0.5012 (OUTLIER) cc_final: 0.4584 (tp) REVERT: A 829 ASP cc_start: 0.3399 (OUTLIER) cc_final: 0.2836 (t70) REVERT: B 87 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.4189 (pmt170) REVERT: B 130 LYS cc_start: 0.7141 (mttt) cc_final: 0.6894 (mmtp) REVERT: B 196 GLU cc_start: 0.7966 (pt0) cc_final: 0.7708 (pt0) REVERT: B 207 LYS cc_start: 0.7949 (mttm) cc_final: 0.7174 (mtmt) REVERT: B 509 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7701 (tttm) REVERT: B 514 GLN cc_start: 0.7953 (tt0) cc_final: 0.7502 (mt0) REVERT: B 653 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 697 TYR cc_start: 0.7763 (m-10) cc_final: 0.7465 (m-80) REVERT: B 710 GLN cc_start: 0.7305 (mp10) cc_final: 0.7084 (mm-40) REVERT: B 738 LEU cc_start: 0.7236 (mp) cc_final: 0.6807 (tp) REVERT: B 759 ILE cc_start: 0.4924 (OUTLIER) cc_final: 0.4557 (tp) REVERT: B 829 ASP cc_start: 0.3419 (OUTLIER) cc_final: 0.2845 (t70) outliers start: 56 outliers final: 26 residues processed: 169 average time/residue: 0.3650 time to fit residues: 69.0111 Evaluate side-chains 145 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 167 GLN A 276 ASN A 350 ASN A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.216802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145415 restraints weight = 12292.166| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.98 r_work: 0.3546 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12694 Z= 0.089 Angle : 0.511 8.126 17220 Z= 0.263 Chirality : 0.043 0.192 1970 Planarity : 0.003 0.032 2180 Dihedral : 5.545 56.145 1719 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.02 % Favored : 94.72 % Rotamer: Outliers : 3.76 % Allowed : 25.35 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: -2.11 (0.22), residues: 1514 helix: -3.18 (0.34), residues: 138 sheet: -2.72 (0.32), residues: 270 loop : -0.79 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.011 0.001 TYR A 233 PHE 0.011 0.001 PHE B 507 TRP 0.010 0.001 TRP B 793 HIS 0.003 0.000 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00196 (12678) covalent geometry : angle 0.51114 (17188) SS BOND : bond 0.00241 ( 16) SS BOND : angle 0.66714 ( 32) hydrogen bonds : bond 0.02429 ( 88) hydrogen bonds : angle 4.91048 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7059 (mttt) cc_final: 0.6821 (mmtp) REVERT: A 207 LYS cc_start: 0.7766 (mttm) cc_final: 0.6998 (mtmt) REVERT: A 514 GLN cc_start: 0.7912 (tt0) cc_final: 0.7452 (mt0) REVERT: A 636 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5418 (ttp-170) REVERT: A 653 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 697 TYR cc_start: 0.7637 (m-10) cc_final: 0.7387 (m-80) REVERT: A 710 GLN cc_start: 0.7678 (mp10) cc_final: 0.7168 (mm-40) REVERT: A 723 ARG cc_start: 0.7218 (tpt90) cc_final: 0.6847 (mmm160) REVERT: A 738 LEU cc_start: 0.7221 (mp) cc_final: 0.6800 (tp) REVERT: A 759 ILE cc_start: 0.4990 (OUTLIER) cc_final: 0.4626 (tp) REVERT: A 829 ASP cc_start: 0.3711 (OUTLIER) cc_final: 0.3093 (t70) REVERT: B 87 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.4188 (pmt170) REVERT: B 130 LYS cc_start: 0.7042 (mttt) cc_final: 0.6764 (mtpp) REVERT: B 196 GLU cc_start: 0.7894 (pt0) cc_final: 0.7614 (pt0) REVERT: B 207 LYS cc_start: 0.7784 (mttm) cc_final: 0.7005 (mtmt) REVERT: B 509 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7619 (tttp) REVERT: B 514 GLN cc_start: 0.7910 (tt0) cc_final: 0.7435 (mt0) REVERT: B 653 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 697 TYR cc_start: 0.7738 (m-10) cc_final: 0.7457 (m-80) REVERT: B 734 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: B 738 LEU cc_start: 0.7232 (mp) cc_final: 0.6940 (tp) REVERT: B 759 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4593 (tp) REVERT: B 761 MET cc_start: 0.4074 (OUTLIER) cc_final: 0.2760 (ppp) REVERT: B 829 ASP cc_start: 0.3327 (OUTLIER) cc_final: 0.2826 (t70) outliers start: 54 outliers final: 26 residues processed: 166 average time/residue: 0.3476 time to fit residues: 64.7274 Evaluate side-chains 143 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 734 GLN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 45 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 167 GLN A 276 ASN A 732 ASN A 781 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138806 restraints weight = 12325.169| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.80 r_work: 0.3518 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12694 Z= 0.164 Angle : 0.577 8.826 17220 Z= 0.293 Chirality : 0.045 0.138 1970 Planarity : 0.003 0.033 2180 Dihedral : 5.904 55.629 1718 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.01 % Favored : 93.59 % Rotamer: Outliers : 4.32 % Allowed : 25.07 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -1.98 (0.22), residues: 1514 helix: -3.09 (0.37), residues: 126 sheet: -2.68 (0.33), residues: 272 loop : -0.72 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 636 TYR 0.017 0.002 TYR A 233 PHE 0.012 0.001 PHE A 325 TRP 0.008 0.001 TRP B 793 HIS 0.010 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00389 (12678) covalent geometry : angle 0.57706 (17188) SS BOND : bond 0.00333 ( 16) SS BOND : angle 0.64497 ( 32) hydrogen bonds : bond 0.02794 ( 88) hydrogen bonds : angle 4.94397 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7183 (mttt) cc_final: 0.6912 (mmtp) REVERT: A 196 GLU cc_start: 0.7943 (pt0) cc_final: 0.7655 (pt0) REVERT: A 509 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7684 (tttm) REVERT: A 514 GLN cc_start: 0.7972 (tt0) cc_final: 0.7537 (mt0) REVERT: A 636 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5489 (ttp-170) REVERT: A 653 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 697 TYR cc_start: 0.7645 (m-10) cc_final: 0.7394 (m-80) REVERT: A 710 GLN cc_start: 0.7694 (mp10) cc_final: 0.7190 (mm-40) REVERT: A 723 ARG cc_start: 0.7368 (tpt90) cc_final: 0.6971 (mmm160) REVERT: A 738 LEU cc_start: 0.7255 (mp) cc_final: 0.6962 (tp) REVERT: A 759 ILE cc_start: 0.4942 (OUTLIER) cc_final: 0.4544 (tp) REVERT: A 761 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.3015 (ppp) REVERT: A 829 ASP cc_start: 0.3636 (OUTLIER) cc_final: 0.2962 (t70) REVERT: B 87 ARG cc_start: 0.4378 (OUTLIER) cc_final: 0.4141 (pmt170) REVERT: B 130 LYS cc_start: 0.7178 (mttt) cc_final: 0.6879 (mtpp) REVERT: B 196 GLU cc_start: 0.7894 (pt0) cc_final: 0.7597 (pt0) REVERT: B 207 LYS cc_start: 0.7981 (mttm) cc_final: 0.7210 (mtmt) REVERT: B 509 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7701 (tttm) REVERT: B 514 GLN cc_start: 0.7970 (tt0) cc_final: 0.7521 (mt0) REVERT: B 653 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7748 (mt-10) REVERT: B 697 TYR cc_start: 0.7760 (m-10) cc_final: 0.7379 (m-10) REVERT: B 738 LEU cc_start: 0.7238 (mp) cc_final: 0.6905 (tp) REVERT: B 759 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4530 (tp) REVERT: B 761 MET cc_start: 0.4237 (OUTLIER) cc_final: 0.2835 (ppp) REVERT: B 829 ASP cc_start: 0.3514 (OUTLIER) cc_final: 0.2856 (t70) outliers start: 62 outliers final: 30 residues processed: 165 average time/residue: 0.3260 time to fit residues: 60.7914 Evaluate side-chains 149 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 167 GLN A 276 ASN A 732 ASN A 781 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN B 781 HIS ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142118 restraints weight = 12250.074| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.76 r_work: 0.3532 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12694 Z= 0.140 Angle : 0.564 8.473 17220 Z= 0.286 Chirality : 0.045 0.144 1970 Planarity : 0.003 0.034 2180 Dihedral : 5.815 56.158 1718 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.48 % Favored : 94.25 % Rotamer: Outliers : 3.97 % Allowed : 25.84 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -1.96 (0.22), residues: 1514 helix: -3.02 (0.38), residues: 126 sheet: -2.73 (0.33), residues: 272 loop : -0.69 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 636 TYR 0.014 0.001 TYR A 233 PHE 0.012 0.001 PHE A 742 TRP 0.009 0.001 TRP B 793 HIS 0.011 0.001 HIS B 781 Details of bonding type rmsd covalent geometry : bond 0.00329 (12678) covalent geometry : angle 0.56084 (17188) SS BOND : bond 0.00373 ( 16) SS BOND : angle 1.46919 ( 32) hydrogen bonds : bond 0.02667 ( 88) hydrogen bonds : angle 4.88251 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 107 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.2953 (mmt) cc_final: 0.2712 (mpp) REVERT: A 130 LYS cc_start: 0.7200 (mttt) cc_final: 0.6940 (mmtp) REVERT: A 196 GLU cc_start: 0.7927 (pt0) cc_final: 0.7635 (pt0) REVERT: A 509 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7674 (tttm) REVERT: A 636 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.5506 (ttp-170) REVERT: A 653 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 697 TYR cc_start: 0.7662 (m-10) cc_final: 0.7240 (m-80) REVERT: A 710 GLN cc_start: 0.7707 (mp10) cc_final: 0.7370 (mp10) REVERT: A 734 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: A 738 LEU cc_start: 0.7136 (mp) cc_final: 0.6924 (tp) REVERT: A 759 ILE cc_start: 0.4949 (OUTLIER) cc_final: 0.4533 (tp) REVERT: A 829 ASP cc_start: 0.3593 (OUTLIER) cc_final: 0.2974 (t70) REVERT: B 130 LYS cc_start: 0.7200 (mttt) cc_final: 0.6922 (mtpp) REVERT: B 196 GLU cc_start: 0.7869 (pt0) cc_final: 0.7593 (pt0) REVERT: B 207 LYS cc_start: 0.7970 (mttm) cc_final: 0.7210 (mtmt) REVERT: B 509 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7673 (tttm) REVERT: B 514 GLN cc_start: 0.7969 (tt0) cc_final: 0.7526 (mt0) REVERT: B 653 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 697 TYR cc_start: 0.7769 (m-10) cc_final: 0.7418 (m-10) REVERT: B 738 LEU cc_start: 0.7370 (mp) cc_final: 0.7116 (tp) REVERT: B 759 ILE cc_start: 0.4834 (OUTLIER) cc_final: 0.4411 (tp) REVERT: B 761 MET cc_start: 0.4303 (OUTLIER) cc_final: 0.2993 (ppp) REVERT: B 829 ASP cc_start: 0.3638 (OUTLIER) cc_final: 0.2937 (t70) outliers start: 57 outliers final: 28 residues processed: 156 average time/residue: 0.3543 time to fit residues: 62.0665 Evaluate side-chains 141 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 144 GLN A 167 GLN A 276 ASN A 732 ASN A 781 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 781 HIS ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142176 restraints weight = 12221.172| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.02 r_work: 0.3488 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12694 Z= 0.165 Angle : 0.582 8.760 17220 Z= 0.294 Chirality : 0.046 0.138 1970 Planarity : 0.003 0.035 2180 Dihedral : 5.961 56.160 1718 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.08 % Favored : 93.53 % Rotamer: Outliers : 3.55 % Allowed : 26.39 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -1.94 (0.22), residues: 1514 helix: -3.02 (0.37), residues: 126 sheet: -2.67 (0.33), residues: 272 loop : -0.69 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.016 0.001 TYR A 233 PHE 0.012 0.001 PHE A 382 TRP 0.008 0.001 TRP B 793 HIS 0.011 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00391 (12678) covalent geometry : angle 0.57942 (17188) SS BOND : bond 0.00338 ( 16) SS BOND : angle 1.32270 ( 32) hydrogen bonds : bond 0.02801 ( 88) hydrogen bonds : angle 4.88849 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7118 (mttt) cc_final: 0.6850 (mmtp) REVERT: A 196 GLU cc_start: 0.7940 (pt0) cc_final: 0.7618 (pt0) REVERT: A 509 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: A 514 GLN cc_start: 0.7956 (tt0) cc_final: 0.7469 (mt0) REVERT: A 636 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5462 (ttp-170) REVERT: A 653 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 697 TYR cc_start: 0.7576 (m-10) cc_final: 0.7312 (m-80) REVERT: A 710 GLN cc_start: 0.7671 (mp10) cc_final: 0.7327 (mp10) REVERT: A 734 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6819 (mp10) REVERT: A 738 LEU cc_start: 0.7278 (mp) cc_final: 0.7054 (tp) REVERT: A 759 ILE cc_start: 0.5028 (OUTLIER) cc_final: 0.4555 (tp) REVERT: A 781 HIS cc_start: 0.4898 (OUTLIER) cc_final: 0.4411 (p90) REVERT: A 829 ASP cc_start: 0.3577 (OUTLIER) cc_final: 0.2898 (t70) REVERT: B 130 LYS cc_start: 0.7121 (mttt) cc_final: 0.6825 (mtpp) REVERT: B 196 GLU cc_start: 0.7841 (pt0) cc_final: 0.7532 (pt0) REVERT: B 509 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7619 (tttm) REVERT: B 514 GLN cc_start: 0.7942 (tt0) cc_final: 0.7454 (mt0) REVERT: B 653 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 697 TYR cc_start: 0.7729 (m-10) cc_final: 0.7386 (m-10) REVERT: B 743 LEU cc_start: 0.6841 (mt) cc_final: 0.6626 (mt) REVERT: B 759 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4534 (tp) REVERT: B 761 MET cc_start: 0.4312 (OUTLIER) cc_final: 0.2974 (ppp) REVERT: B 781 HIS cc_start: 0.4900 (OUTLIER) cc_final: 0.4404 (p90) REVERT: B 829 ASP cc_start: 0.3611 (OUTLIER) cc_final: 0.2938 (t70) outliers start: 51 outliers final: 30 residues processed: 149 average time/residue: 0.3408 time to fit residues: 57.0086 Evaluate side-chains 144 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 781 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 129 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 167 GLN A 276 ASN A 732 ASN A 781 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.216102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144686 restraints weight = 12284.540| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.01 r_work: 0.3495 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12694 Z= 0.135 Angle : 0.567 8.492 17220 Z= 0.286 Chirality : 0.045 0.138 1970 Planarity : 0.003 0.034 2180 Dihedral : 5.870 56.506 1718 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 3.27 % Allowed : 26.46 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -1.92 (0.22), residues: 1514 helix: -3.01 (0.38), residues: 126 sheet: -2.67 (0.33), residues: 272 loop : -0.67 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 636 TYR 0.014 0.001 TYR B 233 PHE 0.011 0.001 PHE B 507 TRP 0.008 0.001 TRP B 793 HIS 0.016 0.001 HIS B 781 Details of bonding type rmsd covalent geometry : bond 0.00316 (12678) covalent geometry : angle 0.56521 (17188) SS BOND : bond 0.00283 ( 16) SS BOND : angle 1.10654 ( 32) hydrogen bonds : bond 0.02654 ( 88) hydrogen bonds : angle 4.83581 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.7160 (mttt) cc_final: 0.6902 (mmtp) REVERT: A 196 GLU cc_start: 0.7963 (pt0) cc_final: 0.7648 (pt0) REVERT: A 509 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7648 (tttm) REVERT: A 514 GLN cc_start: 0.7937 (tt0) cc_final: 0.7480 (mt0) REVERT: A 636 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5501 (ttp-170) REVERT: A 653 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 697 TYR cc_start: 0.7582 (m-10) cc_final: 0.7306 (m-80) REVERT: A 734 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: A 759 ILE cc_start: 0.5076 (OUTLIER) cc_final: 0.4604 (tp) REVERT: A 829 ASP cc_start: 0.3557 (OUTLIER) cc_final: 0.2842 (t70) REVERT: B 130 LYS cc_start: 0.7163 (mttt) cc_final: 0.6878 (mtpp) REVERT: B 196 GLU cc_start: 0.7878 (pt0) cc_final: 0.7564 (pt0) REVERT: B 243 ASP cc_start: 0.7608 (m-30) cc_final: 0.7351 (m-30) REVERT: B 246 ASN cc_start: 0.8217 (m-40) cc_final: 0.7765 (m110) REVERT: B 509 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7642 (tttm) REVERT: B 514 GLN cc_start: 0.7958 (tt0) cc_final: 0.7483 (mt0) REVERT: B 653 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 697 TYR cc_start: 0.7738 (m-10) cc_final: 0.7388 (m-10) REVERT: B 743 LEU cc_start: 0.6811 (mt) cc_final: 0.6597 (mt) REVERT: B 759 ILE cc_start: 0.5049 (OUTLIER) cc_final: 0.4570 (tp) REVERT: B 761 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.3007 (ppp) REVERT: B 829 ASP cc_start: 0.3614 (OUTLIER) cc_final: 0.2917 (t70) outliers start: 47 outliers final: 29 residues processed: 144 average time/residue: 0.3321 time to fit residues: 54.2543 Evaluate side-chains 138 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 731 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 829 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 121 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 167 GLN A 276 ASN A 732 ASN A 781 HIS B 167 GLN B 276 ASN B 350 ASN B 604 ASN B 676 ASN B 781 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.217743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144244 restraints weight = 12286.249| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.80 r_work: 0.3585 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12694 Z= 0.085 Angle : 0.524 8.000 17220 Z= 0.266 Chirality : 0.043 0.134 1970 Planarity : 0.003 0.034 2180 Dihedral : 5.409 56.592 1718 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.69 % Favored : 95.05 % Rotamer: Outliers : 2.79 % Allowed : 26.95 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: -1.98 (0.22), residues: 1514 helix: -3.11 (0.34), residues: 148 sheet: -2.57 (0.33), residues: 270 loop : -0.69 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 121 TYR 0.012 0.001 TYR A 546 PHE 0.013 0.001 PHE B 507 TRP 0.009 0.001 TRP B 793 HIS 0.013 0.001 HIS B 781 Details of bonding type rmsd covalent geometry : bond 0.00187 (12678) covalent geometry : angle 0.52321 (17188) SS BOND : bond 0.00179 ( 16) SS BOND : angle 0.76161 ( 32) hydrogen bonds : bond 0.02187 ( 88) hydrogen bonds : angle 4.55276 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.97 seconds wall clock time: 75 minutes 21.53 seconds (4521.53 seconds total)