Starting phenix.real_space_refine on Wed Jul 30 11:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lw1_30002/07_2025/6lw1_30002.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lw1_30002/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lw1_30002/07_2025/6lw1_30002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lw1_30002/07_2025/6lw1_30002.map" model { file = "/net/cci-nas-00/data/ceres_data/6lw1_30002/07_2025/6lw1_30002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lw1_30002/07_2025/6lw1_30002.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 14.60, per 1000 atoms: 1.18 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: 2.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.37 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: 3.82 Time building geometry restraints manager: 3.26 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: 0.06 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.680 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.140 ------------------------------------------------------------------------------- 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 : 11.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B 793 HIS 0.006 0.001 HIS B 298 PHE 0.016 0.002 PHE A 96 TYR 0.020 0.002 TYR B 233 ARG 0.007 0.001 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.29303 ( 88) hydrogen bonds : angle 8.27823 ( 174) SS BOND : bond 0.00674 ( 16) SS BOND : angle 1.42401 ( 32) covalent geometry : bond 0.00886 (12678) covalent geometry : angle 0.90810 (17188) *********************** 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 : 2.027 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: 0.4430 (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: 0.7358 (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: 0.8955 time to fit residues: 235.1902 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 : 1.437 ------------------------------------------------------------------------------- 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 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 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 275 ASN 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 ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.213775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140836 restraints weight = 12228.076| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.04 r_work: 0.3525 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12694 Z= 0.112 Angle : 0.602 9.072 17220 Z= 0.306 Chirality : 0.045 0.140 1970 Planarity : 0.003 0.032 2180 Dihedral : 7.709 58.001 1766 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 5.22 % Allowed : 23.05 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1514 helix: -3.90 (0.29), residues: 114 sheet: -3.23 (0.31), residues: 268 loop : -1.39 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 793 HIS 0.003 0.001 HIS B 46 PHE 0.015 0.001 PHE B 664 TYR 0.010 0.001 TYR B 233 ARG 0.006 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 88) hydrogen bonds : angle 6.25755 ( 174) SS BOND : bond 0.00393 ( 16) SS BOND : angle 0.68594 ( 32) covalent geometry : bond 0.00249 (12678) covalent geometry : angle 0.60194 (17188) *********************** 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 206 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 131 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7818 (mttm) cc_final: 0.7054 (mtmt) REVERT: A 509 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7615 (tttm) REVERT: A 510 SER cc_start: 0.8535 (p) cc_final: 0.8263 (t) REVERT: A 514 GLN cc_start: 0.7949 (tt0) cc_final: 0.7516 (mt0) REVERT: A 653 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 723 ARG cc_start: 0.7174 (tpt90) cc_final: 0.6825 (mmm160) REVERT: A 734 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: A 759 ILE cc_start: 0.4784 (OUTLIER) cc_final: 0.4186 (tp) REVERT: A 782 HIS cc_start: 0.5923 (OUTLIER) cc_final: 0.5365 (m170) REVERT: A 829 ASP cc_start: 0.3373 (OUTLIER) cc_final: 0.2772 (t70) REVERT: B 87 ARG cc_start: 0.4363 (OUTLIER) cc_final: 0.4094 (pmt170) REVERT: B 95 ASP cc_start: 0.7405 (t0) cc_final: 0.6975 (t70) REVERT: B 130 LYS cc_start: 0.7089 (mttt) cc_final: 0.6869 (mmtp) REVERT: B 207 LYS cc_start: 0.7916 (mttm) cc_final: 0.7066 (mtmt) REVERT: B 509 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7605 (tttm) REVERT: B 510 SER cc_start: 0.8496 (p) cc_final: 0.8293 (t) REVERT: B 514 GLN cc_start: 0.7905 (tt0) cc_final: 0.7418 (mt0) REVERT: B 653 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 697 TYR cc_start: 0.7664 (m-10) cc_final: 0.7330 (m-80) REVERT: B 710 GLN cc_start: 0.7529 (mp10) cc_final: 0.7287 (mp10) REVERT: B 723 ARG cc_start: 0.7392 (tpt90) cc_final: 0.6898 (mmm160) REVERT: B 727 ASN cc_start: 0.6915 (OUTLIER) cc_final: 0.6589 (m-40) REVERT: B 734 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6807 (mp10) REVERT: B 759 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4155 (tp) REVERT: B 782 HIS cc_start: 0.6029 (OUTLIER) cc_final: 0.5396 (m170) REVERT: B 829 ASP cc_start: 0.3432 (OUTLIER) cc_final: 0.2775 (t70) outliers start: 75 outliers final: 27 residues processed: 198 average time/residue: 0.8410 time to fit residues: 188.8487 Evaluate side-chains 158 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 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 739 THR 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 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 714 VAL Chi-restraints excluded: chain B residue 727 ASN 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 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 89 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 77 optimal weight: 0.0270 chunk 143 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 276 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 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 604 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 = 0.4335 r_free = 0.4335 target = 0.209186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134464 restraints weight = 12366.970| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.77 r_work: 0.3472 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12694 Z= 0.296 Angle : 0.701 10.345 17220 Z= 0.352 Chirality : 0.049 0.146 1970 Planarity : 0.004 0.035 2180 Dihedral : 6.969 55.592 1724 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.12 % Favored : 91.48 % Rotamer: Outliers : 6.20 % Allowed : 23.96 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.21), residues: 1514 helix: -3.73 (0.32), residues: 114 sheet: -3.08 (0.31), residues: 268 loop : -1.24 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.006 0.001 HIS B 298 PHE 0.015 0.002 PHE A 325 TYR 0.016 0.002 TYR B 233 ARG 0.004 0.001 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 88) hydrogen bonds : angle 6.04097 ( 174) SS BOND : bond 0.00734 ( 16) SS BOND : angle 1.02573 ( 32) covalent geometry : bond 0.00709 (12678) covalent geometry : angle 0.70061 (17188) *********************** 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 215 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 126 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7715 (mtmm) REVERT: A 510 SER cc_start: 0.8564 (p) cc_final: 0.8262 (t) REVERT: A 514 GLN cc_start: 0.8016 (tt0) cc_final: 0.7576 (mt0) REVERT: A 653 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 696 ARG cc_start: 0.7179 (tmm160) cc_final: 0.6951 (tmm160) REVERT: A 710 GLN cc_start: 0.7745 (mp10) cc_final: 0.7353 (mp10) REVERT: A 734 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: A 759 ILE cc_start: 0.4830 (OUTLIER) cc_final: 0.4177 (tp) REVERT: A 829 ASP cc_start: 0.3663 (OUTLIER) cc_final: 0.3062 (t70) REVERT: B 87 ARG cc_start: 0.4484 (OUTLIER) cc_final: 0.4168 (pmt170) REVERT: B 130 LYS cc_start: 0.7291 (mttt) cc_final: 0.7054 (mmtp) REVERT: B 207 LYS cc_start: 0.8168 (mttm) cc_final: 0.7369 (mtmt) REVERT: B 509 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7606 (tttm) REVERT: B 510 SER cc_start: 0.8550 (p) cc_final: 0.8316 (t) REVERT: B 514 GLN cc_start: 0.8009 (tt0) cc_final: 0.7562 (mt0) REVERT: B 653 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 673 MET cc_start: 0.8410 (mmt) cc_final: 0.7682 (mtp) REVERT: B 697 TYR cc_start: 0.7704 (m-10) cc_final: 0.7348 (m-10) REVERT: B 727 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6921 (m-40) REVERT: B 734 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: B 759 ILE cc_start: 0.4832 (OUTLIER) cc_final: 0.4217 (tp) REVERT: B 829 ASP cc_start: 0.3782 (OUTLIER) cc_final: 0.3184 (t70) outliers start: 89 outliers final: 46 residues processed: 201 average time/residue: 0.8130 time to fit residues: 185.3500 Evaluate side-chains 174 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 184 TYR Chi-restraints excluded: chain A residue 218 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 521 CYS 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 603 MET 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 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 755 SER 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 810 THR 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 184 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 MET 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 474 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 521 CYS 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 610 SER Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 731 LYS 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 755 SER 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 810 THR 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 83 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 66 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN B 732 ASN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.213981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139718 restraints weight = 12252.627| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.79 r_work: 0.3506 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12694 Z= 0.161 Angle : 0.588 9.127 17220 Z= 0.301 Chirality : 0.045 0.140 1970 Planarity : 0.003 0.032 2180 Dihedral : 6.488 56.494 1724 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.47 % Favored : 93.13 % Rotamer: Outliers : 5.43 % Allowed : 25.00 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1514 helix: -3.52 (0.33), residues: 114 sheet: -2.98 (0.31), residues: 272 loop : -1.07 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.004 0.001 HIS B 298 PHE 0.012 0.001 PHE B 507 TYR 0.015 0.001 TYR B 233 ARG 0.004 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 88) hydrogen bonds : angle 5.77484 ( 174) SS BOND : bond 0.00538 ( 16) SS BOND : angle 0.88785 ( 32) covalent geometry : bond 0.00379 (12678) covalent geometry : angle 0.58773 (17188) *********************** 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 199 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 121 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 509 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7626 (tttm) REVERT: A 510 SER cc_start: 0.8554 (p) cc_final: 0.8278 (t) REVERT: A 514 GLN cc_start: 0.7962 (tt0) cc_final: 0.7506 (mt0) REVERT: A 653 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 710 GLN cc_start: 0.7699 (mp10) cc_final: 0.7289 (mp10) REVERT: A 723 ARG cc_start: 0.7220 (tpt90) cc_final: 0.6885 (mmm160) REVERT: A 759 ILE cc_start: 0.4863 (OUTLIER) cc_final: 0.4197 (tp) REVERT: A 829 ASP cc_start: 0.3457 (OUTLIER) cc_final: 0.2877 (t70) REVERT: B 87 ARG cc_start: 0.4400 (OUTLIER) cc_final: 0.4085 (pmt170) REVERT: B 130 LYS cc_start: 0.7244 (mttt) cc_final: 0.6919 (mtpp) REVERT: B 207 LYS cc_start: 0.8073 (mttm) cc_final: 0.7239 (mtmt) REVERT: B 509 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7617 (tttm) REVERT: B 510 SER cc_start: 0.8514 (p) cc_final: 0.8305 (t) REVERT: B 514 GLN cc_start: 0.7971 (tt0) cc_final: 0.7523 (mt0) REVERT: B 653 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 697 TYR cc_start: 0.7699 (m-10) cc_final: 0.7348 (m-10) REVERT: B 727 ASN cc_start: 0.7174 (OUTLIER) cc_final: 0.6803 (m-40) REVERT: B 734 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: B 759 ILE cc_start: 0.4866 (OUTLIER) cc_final: 0.4188 (tp) REVERT: B 829 ASP cc_start: 0.3586 (OUTLIER) cc_final: 0.3004 (t70) outliers start: 78 outliers final: 32 residues processed: 187 average time/residue: 0.8298 time to fit residues: 175.8133 Evaluate side-chains 155 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 291 GLU 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 550 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET 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 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 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 594 ASN Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 727 ASN 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 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 84 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 151 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 66 ASN ** B 99 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 = 0.4329 r_free = 0.4329 target = 0.208570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133438 restraints weight = 12303.375| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.80 r_work: 0.3456 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 12694 Z= 0.335 Angle : 0.714 10.229 17220 Z= 0.358 Chirality : 0.051 0.150 1970 Planarity : 0.004 0.037 2180 Dihedral : 6.944 55.593 1722 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.65 % Favored : 90.95 % Rotamer: Outliers : 6.75 % Allowed : 23.96 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.22), residues: 1514 helix: -3.67 (0.31), residues: 126 sheet: -2.60 (0.36), residues: 236 loop : -1.24 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 793 HIS 0.006 0.001 HIS B 298 PHE 0.015 0.002 PHE A 325 TYR 0.019 0.002 TYR A 233 ARG 0.005 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 88) hydrogen bonds : angle 5.81932 ( 174) SS BOND : bond 0.00615 ( 16) SS BOND : angle 0.73027 ( 32) covalent geometry : bond 0.00803 (12678) covalent geometry : angle 0.71389 (17188) *********************** 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 213 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 116 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LYS cc_start: 0.6915 (ttmt) cc_final: 0.6370 (mtpt) REVERT: A 509 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7794 (mtmm) REVERT: A 510 SER cc_start: 0.8566 (p) cc_final: 0.8242 (t) REVERT: A 653 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 678 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.6859 (mttp) REVERT: A 710 GLN cc_start: 0.7812 (mp10) cc_final: 0.7435 (mp10) REVERT: A 734 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: A 759 ILE cc_start: 0.4799 (OUTLIER) cc_final: 0.4417 (tp) REVERT: A 829 ASP cc_start: 0.3496 (OUTLIER) cc_final: 0.2869 (t70) REVERT: B 130 LYS cc_start: 0.7225 (mttt) cc_final: 0.6976 (mmtp) REVERT: B 170 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: B 196 GLU cc_start: 0.7967 (pt0) cc_final: 0.7665 (pt0) REVERT: B 509 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7566 (tttm) REVERT: B 510 SER cc_start: 0.8545 (p) cc_final: 0.8270 (t) REVERT: B 602 MET cc_start: 0.8967 (mtm) cc_final: 0.8651 (mpp) REVERT: B 653 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7752 (mt-10) REVERT: B 673 MET cc_start: 0.8269 (mmt) cc_final: 0.7637 (mtp) REVERT: B 678 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.6846 (mttp) REVERT: B 697 TYR cc_start: 0.7717 (m-10) cc_final: 0.7366 (m-10) REVERT: B 727 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6875 (m-40) REVERT: B 759 ILE cc_start: 0.4850 (OUTLIER) cc_final: 0.4585 (tp) REVERT: B 829 ASP cc_start: 0.3524 (OUTLIER) cc_final: 0.2887 (t70) outliers start: 97 outliers final: 53 residues processed: 204 average time/residue: 0.8298 time to fit residues: 192.1499 Evaluate side-chains 178 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 114 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 184 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 322 SER 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 474 SER 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 603 MET Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 678 LYS 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 740 LYS Chi-restraints excluded: chain A residue 755 SER 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 810 THR 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 170 GLU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 289 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 474 SER Chi-restraints excluded: chain B residue 490 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 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 755 SER 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 810 THR 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 151 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN 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 66 ASN B 99 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN B 732 ASN ** 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 = 0.4395 r_free = 0.4395 target = 0.215710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141930 restraints weight = 12317.100| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.89 r_work: 0.3499 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12694 Z= 0.109 Angle : 0.551 8.501 17220 Z= 0.284 Chirality : 0.044 0.136 1970 Planarity : 0.003 0.031 2180 Dihedral : 6.182 56.979 1722 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.22 % Favored : 94.52 % Rotamer: Outliers : 3.90 % Allowed : 26.95 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.22), residues: 1514 helix: -3.26 (0.36), residues: 114 sheet: -2.45 (0.37), residues: 236 loop : -1.01 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 793 HIS 0.003 0.000 HIS A 298 PHE 0.013 0.001 PHE B 507 TYR 0.014 0.001 TYR A 546 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 88) hydrogen bonds : angle 5.49278 ( 174) SS BOND : bond 0.00161 ( 16) SS BOND : angle 0.97092 ( 32) covalent geometry : bond 0.00250 (12678) covalent geometry : angle 0.55006 (17188) *********************** 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 167 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 CYS cc_start: 0.6279 (m) cc_final: 0.5759 (m) REVERT: A 291 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: A 509 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7599 (tttm) REVERT: A 510 SER cc_start: 0.8533 (p) cc_final: 0.8281 (t) REVERT: A 653 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 710 GLN cc_start: 0.7713 (mp10) cc_final: 0.7427 (mp10) REVERT: A 723 ARG cc_start: 0.7319 (tpt90) cc_final: 0.6927 (mmm160) REVERT: A 738 LEU cc_start: 0.7455 (mp) cc_final: 0.7234 (tp) REVERT: A 759 ILE cc_start: 0.4764 (OUTLIER) cc_final: 0.4403 (tp) REVERT: A 829 ASP cc_start: 0.3228 (OUTLIER) cc_final: 0.2694 (t70) REVERT: B 130 LYS cc_start: 0.7156 (mttt) cc_final: 0.6840 (mtpp) REVERT: B 196 GLU cc_start: 0.7954 (pt0) cc_final: 0.7670 (pt0) REVERT: B 207 LYS cc_start: 0.7986 (mttm) cc_final: 0.7173 (mtmt) REVERT: B 509 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7562 (tttm) REVERT: B 510 SER cc_start: 0.8489 (p) cc_final: 0.8270 (t) REVERT: B 653 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 673 MET cc_start: 0.8314 (mmt) cc_final: 0.7707 (mtp) REVERT: B 697 TYR cc_start: 0.7731 (m-10) cc_final: 0.7380 (m-10) REVERT: B 727 ASN cc_start: 0.7094 (OUTLIER) cc_final: 0.6718 (m-40) REVERT: B 734 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: B 738 LEU cc_start: 0.7295 (mp) cc_final: 0.7008 (tp) REVERT: B 759 ILE cc_start: 0.4930 (OUTLIER) cc_final: 0.4653 (tp) REVERT: B 829 ASP cc_start: 0.3270 (OUTLIER) cc_final: 0.2720 (t70) outliers start: 56 outliers final: 19 residues processed: 161 average time/residue: 0.8798 time to fit residues: 159.9169 Evaluate side-chains 133 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 291 GLU Chi-restraints excluded: chain A residue 377 ILE 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 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 714 VAL 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 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 406 THR 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 714 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 734 GLN Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 759 ILE 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 77 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 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 = 0.4373 r_free = 0.4373 target = 0.213171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141224 restraints weight = 12260.576| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.01 r_work: 0.3451 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12694 Z= 0.205 Angle : 0.618 9.711 17220 Z= 0.310 Chirality : 0.046 0.140 1970 Planarity : 0.003 0.030 2180 Dihedral : 6.445 56.168 1722 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.07 % Favored : 92.54 % Rotamer: Outliers : 4.39 % Allowed : 26.67 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.22), residues: 1514 helix: -3.19 (0.36), residues: 114 sheet: -2.77 (0.33), residues: 272 loop : -0.89 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 793 HIS 0.005 0.001 HIS A 298 PHE 0.014 0.002 PHE B 325 TYR 0.016 0.002 TYR A 233 ARG 0.003 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 88) hydrogen bonds : angle 5.43305 ( 174) SS BOND : bond 0.00413 ( 16) SS BOND : angle 1.00596 ( 32) covalent geometry : bond 0.00486 (12678) covalent geometry : angle 0.61682 (17188) *********************** 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 173 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 110 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.6163 (t0) REVERT: A 98 CYS cc_start: 0.6165 (m) cc_final: 0.5687 (m) REVERT: A 291 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: A 509 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7789 (mtmm) REVERT: A 510 SER cc_start: 0.8532 (p) cc_final: 0.8263 (t) REVERT: A 673 MET cc_start: 0.8313 (mmt) cc_final: 0.7701 (mtp) REVERT: A 678 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6855 (mttp) REVERT: A 710 GLN cc_start: 0.7783 (mp10) cc_final: 0.7449 (mp10) REVERT: A 738 LEU cc_start: 0.7487 (mp) cc_final: 0.7269 (tp) REVERT: A 759 ILE cc_start: 0.5030 (OUTLIER) cc_final: 0.4562 (tp) REVERT: A 829 ASP cc_start: 0.3276 (OUTLIER) cc_final: 0.2679 (t70) REVERT: B 130 LYS cc_start: 0.7224 (mttt) cc_final: 0.6915 (mtpp) REVERT: B 196 GLU cc_start: 0.7989 (pt0) cc_final: 0.7661 (pt0) REVERT: B 509 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7560 (tttm) REVERT: B 510 SER cc_start: 0.8523 (p) cc_final: 0.8294 (t) REVERT: B 653 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7758 (mt-10) REVERT: B 673 MET cc_start: 0.8345 (mmt) cc_final: 0.7758 (mtp) REVERT: B 697 TYR cc_start: 0.7735 (m-10) cc_final: 0.7382 (m-10) REVERT: B 727 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6753 (m-40) REVERT: B 738 LEU cc_start: 0.7339 (mp) cc_final: 0.6997 (tp) REVERT: B 759 ILE cc_start: 0.4825 (OUTLIER) cc_final: 0.4478 (tp) REVERT: B 761 MET cc_start: 0.4063 (OUTLIER) cc_final: 0.2870 (ppp) REVERT: B 829 ASP cc_start: 0.3313 (OUTLIER) cc_final: 0.2705 (t70) outliers start: 63 outliers final: 36 residues processed: 166 average time/residue: 0.7806 time to fit residues: 147.9571 Evaluate side-chains 154 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 291 GLU Chi-restraints excluded: chain A residue 322 SER 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 678 LYS 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 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 810 THR 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 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 474 SER 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 712 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 727 ASN 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 17 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4389 r_free = 0.4389 target = 0.214978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141693 restraints weight = 12248.060| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.94 r_work: 0.3533 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12694 Z= 0.104 Angle : 0.537 9.139 17220 Z= 0.275 Chirality : 0.043 0.135 1970 Planarity : 0.003 0.031 2180 Dihedral : 5.925 56.989 1722 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.02 % Favored : 94.72 % Rotamer: Outliers : 4.25 % Allowed : 27.02 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1514 helix: -3.11 (0.36), residues: 126 sheet: -2.30 (0.37), residues: 234 loop : -0.89 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 793 HIS 0.003 0.000 HIS A 298 PHE 0.014 0.001 PHE B 507 TYR 0.012 0.001 TYR B 546 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.02591 ( 88) hydrogen bonds : angle 5.16826 ( 174) SS BOND : bond 0.00210 ( 16) SS BOND : angle 0.65699 ( 32) covalent geometry : bond 0.00235 (12678) covalent geometry : angle 0.53634 (17188) *********************** 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 180 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6412 (OUTLIER) cc_final: 0.6101 (t0) REVERT: A 98 CYS cc_start: 0.5946 (m) cc_final: 0.5514 (m) REVERT: A 196 GLU cc_start: 0.7978 (pt0) cc_final: 0.7667 (pt0) REVERT: A 291 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 510 SER cc_start: 0.8477 (p) cc_final: 0.8238 (t) REVERT: A 653 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 710 GLN cc_start: 0.7754 (mp10) cc_final: 0.7223 (mm-40) REVERT: A 734 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6886 (mp10) REVERT: A 829 ASP cc_start: 0.3502 (OUTLIER) cc_final: 0.2889 (t70) REVERT: B 98 CYS cc_start: 0.6069 (m) cc_final: 0.5550 (m) REVERT: B 130 LYS cc_start: 0.7129 (mttt) cc_final: 0.6864 (mtpp) REVERT: B 196 GLU cc_start: 0.7964 (pt0) cc_final: 0.7708 (pt0) REVERT: B 509 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7580 (tttm) REVERT: B 678 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6789 (mttp) REVERT: B 697 TYR cc_start: 0.7744 (m-10) cc_final: 0.7356 (m-10) REVERT: B 727 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6627 (m-40) REVERT: B 738 LEU cc_start: 0.7301 (mp) cc_final: 0.7017 (tp) REVERT: B 759 ILE cc_start: 0.4957 (OUTLIER) cc_final: 0.4668 (tp) REVERT: B 778 LEU cc_start: 0.6357 (tt) cc_final: 0.5867 (mp) REVERT: B 829 ASP cc_start: 0.3347 (OUTLIER) cc_final: 0.2719 (t70) outliers start: 61 outliers final: 27 residues processed: 172 average time/residue: 0.8655 time to fit residues: 168.0978 Evaluate side-chains 147 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 291 GLU Chi-restraints excluded: chain A residue 377 ILE 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 586 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 SER 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 792 VAL 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 135 ASP Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR 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 678 LYS Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 727 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 135 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 76 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 732 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 167 GLN B 276 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 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 = 0.4402 r_free = 0.4402 target = 0.216456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142564 restraints weight = 12261.475| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.80 r_work: 0.3536 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12694 Z= 0.118 Angle : 0.558 8.981 17220 Z= 0.284 Chirality : 0.044 0.233 1970 Planarity : 0.003 0.030 2180 Dihedral : 5.891 56.446 1720 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.61 % Favored : 94.12 % Rotamer: Outliers : 3.62 % Allowed : 27.92 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.22), residues: 1514 helix: -3.05 (0.37), residues: 126 sheet: -2.63 (0.33), residues: 272 loop : -0.72 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 793 HIS 0.003 0.000 HIS B 298 PHE 0.013 0.001 PHE B 507 TYR 0.014 0.001 TYR A 546 ARG 0.002 0.000 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.02635 ( 88) hydrogen bonds : angle 5.03204 ( 174) SS BOND : bond 0.00236 ( 16) SS BOND : angle 0.67288 ( 32) covalent geometry : bond 0.00273 (12678) covalent geometry : angle 0.55798 (17188) *********************** 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 164 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6199 (t0) REVERT: A 98 CYS cc_start: 0.5999 (m) cc_final: 0.5572 (m) REVERT: A 196 GLU cc_start: 0.7933 (pt0) cc_final: 0.7630 (pt0) REVERT: A 291 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 360 MET cc_start: 0.8587 (ttp) cc_final: 0.8371 (tpp) REVERT: A 510 SER cc_start: 0.8459 (p) cc_final: 0.8235 (t) REVERT: A 653 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 710 GLN cc_start: 0.7784 (mp10) cc_final: 0.7285 (mm-40) REVERT: A 829 ASP cc_start: 0.3564 (OUTLIER) cc_final: 0.2875 (t70) REVERT: B 98 CYS cc_start: 0.5904 (m) cc_final: 0.5417 (m) REVERT: B 130 LYS cc_start: 0.7136 (mttt) cc_final: 0.6872 (mtpp) REVERT: B 196 GLU cc_start: 0.7893 (pt0) cc_final: 0.7583 (pt0) REVERT: B 360 MET cc_start: 0.8582 (ttp) cc_final: 0.8368 (tpp) REVERT: B 509 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7641 (tttm) REVERT: B 653 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 678 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6774 (mttp) REVERT: B 697 TYR cc_start: 0.7759 (m-10) cc_final: 0.7369 (m-10) REVERT: B 738 LEU cc_start: 0.7186 (mp) cc_final: 0.6874 (tp) REVERT: B 759 ILE cc_start: 0.5074 (OUTLIER) cc_final: 0.4672 (tp) REVERT: B 778 LEU cc_start: 0.6334 (tt) cc_final: 0.5908 (mp) REVERT: B 829 ASP cc_start: 0.3570 (OUTLIER) cc_final: 0.2904 (t70) outliers start: 52 outliers final: 28 residues processed: 159 average time/residue: 0.8654 time to fit residues: 155.4561 Evaluate side-chains 145 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 291 GLU Chi-restraints excluded: chain A residue 377 ILE 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 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 740 LYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 792 VAL 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 406 THR 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 678 LYS 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 808 LEU Chi-restraints excluded: chain B residue 810 THR 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 43 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 144 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.212671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141401 restraints weight = 12180.456| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.00 r_work: 0.3451 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12694 Z= 0.250 Angle : 0.663 9.515 17220 Z= 0.331 Chirality : 0.049 0.275 1970 Planarity : 0.004 0.032 2180 Dihedral : 6.444 56.545 1720 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.20 % Favored : 92.40 % Rotamer: Outliers : 3.76 % Allowed : 27.86 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1514 helix: -2.95 (0.40), residues: 114 sheet: -2.66 (0.33), residues: 272 loop : -0.77 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 793 HIS 0.005 0.001 HIS A 298 PHE 0.015 0.002 PHE B 325 TYR 0.023 0.002 TYR A 233 ARG 0.004 0.000 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 88) hydrogen bonds : angle 5.22378 ( 174) SS BOND : bond 0.00434 ( 16) SS BOND : angle 0.87074 ( 32) covalent geometry : bond 0.00599 (12678) covalent geometry : angle 0.66272 (17188) ********************** 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 165 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6466 (OUTLIER) cc_final: 0.6158 (t0) REVERT: A 98 CYS cc_start: 0.6181 (m) cc_final: 0.5756 (m) REVERT: A 196 GLU cc_start: 0.7904 (pt0) cc_final: 0.7577 (pt0) REVERT: A 291 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 510 SER cc_start: 0.8501 (p) cc_final: 0.8213 (t) REVERT: A 636 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5725 (ttp-170) REVERT: A 653 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 673 MET cc_start: 0.8268 (mmt) cc_final: 0.7618 (mtp) REVERT: A 710 GLN cc_start: 0.7792 (mp10) cc_final: 0.7280 (mm-40) REVERT: A 829 ASP cc_start: 0.3562 (OUTLIER) cc_final: 0.2849 (t70) REVERT: B 98 CYS cc_start: 0.6021 (m) cc_final: 0.5577 (m) REVERT: B 130 LYS cc_start: 0.7159 (mttt) cc_final: 0.6832 (mtpp) REVERT: B 196 GLU cc_start: 0.7929 (pt0) cc_final: 0.7617 (pt0) REVERT: B 509 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7614 (tttm) REVERT: B 653 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 673 MET cc_start: 0.8330 (mmt) cc_final: 0.7690 (mtp) REVERT: B 678 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6704 (mttp) REVERT: B 697 TYR cc_start: 0.7738 (m-10) cc_final: 0.7369 (m-80) REVERT: B 829 ASP cc_start: 0.3509 (OUTLIER) cc_final: 0.2797 (t70) outliers start: 54 outliers final: 34 residues processed: 159 average time/residue: 0.8637 time to fit residues: 155.9563 Evaluate side-chains 152 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 291 GLU 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 474 SER Chi-restraints excluded: chain A residue 490 SER 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 788 THR Chi-restraints excluded: chain A residue 792 VAL 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 474 SER 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 678 LYS 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 808 LEU Chi-restraints excluded: chain B residue 810 THR 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 67 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 81 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 676 ASN A 732 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142787 restraints weight = 12186.330| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.78 r_work: 0.3540 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12694 Z= 0.111 Angle : 0.560 8.690 17220 Z= 0.285 Chirality : 0.044 0.153 1970 Planarity : 0.003 0.031 2180 Dihedral : 5.910 57.442 1720 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.22 % Favored : 94.52 % Rotamer: Outliers : 3.34 % Allowed : 28.48 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1514 helix: -2.96 (0.38), residues: 126 sheet: -2.63 (0.33), residues: 272 loop : -0.67 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 793 HIS 0.004 0.001 HIS B 298 PHE 0.014 0.001 PHE B 507 TYR 0.013 0.001 TYR A 546 ARG 0.003 0.000 ARG A 717 Details of bonding type rmsd hydrogen bonds : bond 0.02544 ( 88) hydrogen bonds : angle 5.03479 ( 174) SS BOND : bond 0.00250 ( 16) SS BOND : angle 0.63673 ( 32) covalent geometry : bond 0.00252 (12678) covalent geometry : angle 0.55970 (17188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11414.95 seconds wall clock time: 198 minutes 17.74 seconds (11897.74 seconds total)