Starting phenix.real_space_refine on Thu Sep 18 09:17:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3q_38895/09_2025/8y3q_38895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3q_38895/09_2025/8y3q_38895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y3q_38895/09_2025/8y3q_38895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3q_38895/09_2025/8y3q_38895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3q_38895/09_2025/8y3q_38895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3q_38895/09_2025/8y3q_38895.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10056 2.51 5 N 2667 2.21 5 O 2943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15738 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3527 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 406} Chain breaks: 3 Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 910 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "E" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 910 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 910 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 809 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "H" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 809 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "I" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 809 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "B" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3527 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 406} Chain breaks: 3 Chain: "C" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3527 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 406} Chain breaks: 3 Time building chain proxies: 3.98, per 1000 atoms: 0.25 Number of scatterers: 15738 At special positions: 0 Unit cell: (126.26, 129.47, 130.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2943 8.00 N 2667 7.00 C 10056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 109 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 109 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " 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: 1.23 Conformation dependent library (CDL) restraints added in 779.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 36 sheets defined 11.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.575A pdb=" N ARG A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.313A pdb=" N THR D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 89 through 93 removed outlier: 4.307A pdb=" N THR E 93 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 89 through 93 removed outlier: 4.297A pdb=" N THR F 93 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 34 removed outlier: 3.661A pdb=" N TYR G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.675A pdb=" N TYR H 34 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 34 removed outlier: 3.699A pdb=" N TYR I 34 " --> pdb=" O SER I 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.691A pdb=" N ARG B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.659A pdb=" N TYR B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.964A pdb=" N GLU B 339 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.623A pdb=" N ARG C 186 " --> pdb=" O TYR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 220 through 228 removed outlier: 3.667A pdb=" N TYR C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.937A pdb=" N GLU C 339 " --> pdb=" O TRP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 560 through 566 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 77 removed outlier: 3.704A pdb=" N GLU A 73 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 75 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 414 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN A 409 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE A 109 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP A 103 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 417 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE A 101 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET A 104 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.788A pdb=" N ASN A 190 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 158 removed outlier: 6.415A pdb=" N SER A 387 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N SER A 521 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER A 523 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 391 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 237 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 234 through 237 current: chain 'A' and resid 304 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 304 through 314 current: chain 'A' and resid 528 through 534 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 528 through 534 current: chain 'B' and resid 304 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 304 through 314 current: chain 'B' and resid 528 through 534 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 528 through 534 current: chain 'C' and resid 304 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 304 through 314 current: chain 'C' and resid 528 through 534 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 582 removed outlier: 3.550A pdb=" N VAL A 625 " --> pdb=" O TYR A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.701A pdb=" N PHE A 553 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 539 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 607 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 12 current: chain 'D' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 62 current: chain 'D' and resid 113 through 114 Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 62 current: chain 'E' and resid 113 through 114 Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.637A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.815A pdb=" N ALA G 86 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP G 87 " --> pdb=" O GLN G 40 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.697A pdb=" N ASP H 87 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP H 37 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.817A pdb=" N ASP I 87 " --> pdb=" O GLN I 40 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 72 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'B' and resid 327 through 333 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.712A pdb=" N ASN B 190 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.606A pdb=" N TYR B 173 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 126 through 128 Processing sheet with id=AC7, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.479A pdb=" N SER B 387 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER B 521 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 176 through 179 Processing sheet with id=AC9, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AD1, first strand: chain 'B' and resid 550 through 554 removed outlier: 6.249A pdb=" N ASP B 551 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL B 542 " --> pdb=" O ASP B 551 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 553 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 539 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 72 through 77 removed outlier: 3.804A pdb=" N GLU C 73 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASN C 409 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE C 109 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP C 103 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 417 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE C 101 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET C 104 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.822A pdb=" N ASN C 190 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.654A pdb=" N TYR C 173 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AD6, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.390A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER C 523 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 391 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AD8, first strand: chain 'C' and resid 579 through 582 Processing sheet with id=AD9, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.740A pdb=" N PHE C 553 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 539 " --> pdb=" O ASP C 611 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 607 " --> pdb=" O THR C 543 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1101 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: 2.89 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5076 1.34 - 1.46: 3483 1.46 - 1.57: 7518 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 16182 Sorted by residual: bond pdb=" CA TYR B 182 " pdb=" CB TYR B 182 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.58e+00 bond pdb=" CG PRO A 386 " pdb=" CD PRO A 386 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.35e+00 bond pdb=" CA ILE B 350 " pdb=" CB ILE B 350 " ideal model delta sigma weight residual 1.537 1.552 -0.015 1.29e-02 6.01e+03 1.31e+00 bond pdb=" CG PRO B 386 " pdb=" CD PRO B 386 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.30e+00 bond pdb=" CG PRO C 386 " pdb=" CD PRO C 386 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.24e+00 ... (remaining 16177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 21434 1.43 - 2.86: 494 2.86 - 4.30: 87 4.30 - 5.73: 15 5.73 - 7.16: 2 Bond angle restraints: 22032 Sorted by residual: angle pdb=" C SER G 95 " pdb=" CA SER G 95 " pdb=" CB SER G 95 " ideal model delta sigma weight residual 115.89 110.73 5.16 1.32e+00 5.74e-01 1.53e+01 angle pdb=" C SER H 95 " pdb=" CA SER H 95 " pdb=" CB SER H 95 " ideal model delta sigma weight residual 115.89 110.74 5.15 1.32e+00 5.74e-01 1.52e+01 angle pdb=" C SER I 95 " pdb=" CA SER I 95 " pdb=" CB SER I 95 " ideal model delta sigma weight residual 115.89 110.82 5.07 1.32e+00 5.74e-01 1.47e+01 angle pdb=" C GLN H 52 " pdb=" N THR H 53 " pdb=" CA THR H 53 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.85e+00 angle pdb=" C GLU B 370 " pdb=" N PHE B 371 " pdb=" CA PHE B 371 " ideal model delta sigma weight residual 122.21 129.37 -7.16 2.87e+00 1.21e-01 6.22e+00 ... (remaining 22027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8658 17.99 - 35.99: 683 35.99 - 53.98: 90 53.98 - 71.97: 19 71.97 - 89.96: 9 Dihedral angle restraints: 9459 sinusoidal: 3714 harmonic: 5745 Sorted by residual: dihedral pdb=" CB CYS D 101 " pdb=" SG CYS D 101 " pdb=" SG CYS D 109 " pdb=" CB CYS D 109 " ideal model delta sinusoidal sigma weight residual 93.00 145.88 -52.88 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS F 101 " pdb=" SG CYS F 101 " pdb=" SG CYS F 109 " pdb=" CB CYS F 109 " ideal model delta sinusoidal sigma weight residual -86.00 -138.34 52.34 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS E 101 " pdb=" SG CYS E 101 " pdb=" SG CYS E 109 " pdb=" CB CYS E 109 " ideal model delta sinusoidal sigma weight residual -86.00 -130.39 44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 9456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1586 0.036 - 0.072: 513 0.072 - 0.108: 191 0.108 - 0.144: 82 0.144 - 0.180: 4 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA ILE B 350 " pdb=" N ILE B 350 " pdb=" C ILE B 350 " pdb=" CB ILE B 350 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA ILE A 522 " pdb=" N ILE A 522 " pdb=" C ILE A 522 " pdb=" CB ILE A 522 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE B 522 " pdb=" N ILE B 522 " pdb=" C ILE B 522 " pdb=" CB ILE B 522 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2373 not shown) Planarity restraints: 2859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 83 " 0.043 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO C 84 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 83 " 0.029 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 84 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 530 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 531 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " -0.022 5.00e-02 4.00e+02 ... (remaining 2856 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 620 2.72 - 3.27: 13857 3.27 - 3.81: 23441 3.81 - 4.36: 29753 4.36 - 4.90: 53532 Nonbonded interactions: 121203 Sorted by model distance: nonbonded pdb=" OG1 THR B 85 " pdb=" OD1 ASN B 88 " model vdw 2.176 3.040 nonbonded pdb=" OE2 GLU I 7 " pdb=" OG1 THR I 21 " model vdw 2.193 3.040 nonbonded pdb=" OE2 GLU A 185 " pdb=" OH TYR A 224 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU C 185 " pdb=" OH TYR C 224 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU H 7 " pdb=" OG1 THR H 21 " model vdw 2.252 3.040 ... (remaining 121198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.050 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.003 0.040 16191 Z= 0.135 Angle : 0.551 7.159 22050 Z= 0.297 Chirality : 0.045 0.180 2376 Planarity : 0.005 0.066 2859 Dihedral : 12.956 89.963 5778 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.19), residues: 1980 helix: -0.27 (0.64), residues: 78 sheet: 0.43 (0.18), residues: 813 loop : -0.26 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.015 0.001 TYR C 74 PHE 0.020 0.001 PHE C 92 TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00313 (16182) covalent geometry : angle 0.54801 (22032) SS BOND : bond 0.00494 ( 9) SS BOND : angle 2.03470 ( 18) hydrogen bonds : bond 0.18926 ( 419) hydrogen bonds : angle 5.97569 ( 1101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.566 Fit side-chains REVERT: A 133 GLN cc_start: 0.7171 (mm110) cc_final: 0.6813 (mm-40) REVERT: A 231 GLU cc_start: 0.8347 (pt0) cc_final: 0.8077 (pt0) REVERT: A 479 GLN cc_start: 0.7794 (mp10) cc_final: 0.7417 (mm110) REVERT: A 538 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7460 (mtmm) REVERT: A 611 ASP cc_start: 0.7483 (m-30) cc_final: 0.7212 (m-30) REVERT: A 612 THR cc_start: 0.8216 (m) cc_final: 0.7896 (t) REVERT: D 54 ASP cc_start: 0.7510 (m-30) cc_final: 0.7287 (m-30) REVERT: E 38 ARG cc_start: 0.6971 (ptt180) cc_final: 0.6682 (ptt90) REVERT: G 88 TYR cc_start: 0.7772 (m-80) cc_final: 0.7536 (m-80) REVERT: H 84 ASP cc_start: 0.8251 (m-30) cc_final: 0.8012 (m-30) REVERT: I 10 MET cc_start: 0.6675 (mmm) cc_final: 0.6185 (mmt) REVERT: I 77 ILE cc_start: 0.7816 (mt) cc_final: 0.7594 (mp) REVERT: B 89 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7926 (mmmt) REVERT: B 538 LYS cc_start: 0.7412 (mtpt) cc_final: 0.6970 (mttm) REVERT: B 581 MET cc_start: 0.8104 (ttt) cc_final: 0.7877 (ttm) REVERT: C 89 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7713 (mmtm) REVERT: C 128 MET cc_start: 0.7937 (tpp) cc_final: 0.7694 (tpp) REVERT: C 388 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7394 (mtp180) REVERT: C 479 GLN cc_start: 0.7585 (mp10) cc_final: 0.7308 (mm110) outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 0.5550 time to fit residues: 175.1119 Evaluate side-chains 188 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 502 HIS G 6 GLN H 6 GLN H 33 ASN H 40 GLN I 33 ASN B 88 ASN B 244 ASN B 502 HIS C 147 GLN C 244 ASN C 246 HIS C 502 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142553 restraints weight = 17672.916| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.42 r_work: 0.3255 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16191 Z= 0.152 Angle : 0.583 9.090 22050 Z= 0.300 Chirality : 0.047 0.157 2376 Planarity : 0.005 0.052 2859 Dihedral : 4.595 26.633 2177 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.54 % Allowed : 7.49 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.19), residues: 1980 helix: -0.40 (0.62), residues: 81 sheet: 0.38 (0.18), residues: 888 loop : -0.05 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 192 TYR 0.026 0.002 TYR C 203 PHE 0.016 0.002 PHE A 92 TRP 0.011 0.001 TRP E 47 HIS 0.005 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00377 (16182) covalent geometry : angle 0.57918 (22032) SS BOND : bond 0.00701 ( 9) SS BOND : angle 2.26663 ( 18) hydrogen bonds : bond 0.03462 ( 419) hydrogen bonds : angle 4.97394 ( 1101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.623 Fit side-chains REVERT: A 133 GLN cc_start: 0.7711 (mm110) cc_final: 0.7351 (mm-40) REVERT: A 305 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6362 (m-30) REVERT: A 479 GLN cc_start: 0.8112 (mp10) cc_final: 0.7761 (mm110) REVERT: A 498 MET cc_start: 0.8347 (mmt) cc_final: 0.8131 (mmm) REVERT: A 509 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.6919 (pp30) REVERT: A 511 ARG cc_start: 0.7894 (mmp-170) cc_final: 0.6770 (mmp-170) REVERT: A 538 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7325 (mtmm) REVERT: A 539 ASN cc_start: 0.8153 (m-40) cc_final: 0.7691 (m-40) REVERT: A 611 ASP cc_start: 0.8040 (m-30) cc_final: 0.7774 (m-30) REVERT: A 612 THR cc_start: 0.8272 (m) cc_final: 0.7899 (t) REVERT: F 20 LEU cc_start: 0.8297 (mt) cc_final: 0.8023 (mp) REVERT: G 88 TYR cc_start: 0.7666 (m-80) cc_final: 0.7417 (m-80) REVERT: B 89 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8043 (mmmt) REVERT: B 104 MET cc_start: 0.8193 (mpp) cc_final: 0.7764 (mmt) REVERT: B 163 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: B 334 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6931 (mtm110) REVERT: B 538 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7074 (mttm) REVERT: B 539 ASN cc_start: 0.8156 (m-40) cc_final: 0.7842 (m-40) REVERT: C 89 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7926 (mmtp) REVERT: C 128 MET cc_start: 0.8262 (tpp) cc_final: 0.7935 (mmm) REVERT: C 333 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7093 (mt) REVERT: C 388 ARG cc_start: 0.8294 (mtm180) cc_final: 0.8085 (mtp180) REVERT: C 479 GLN cc_start: 0.8010 (mp10) cc_final: 0.7622 (mm110) REVERT: C 541 SER cc_start: 0.7611 (OUTLIER) cc_final: 0.7193 (t) REVERT: C 612 THR cc_start: 0.8659 (m) cc_final: 0.8451 (t) outliers start: 61 outliers final: 30 residues processed: 250 average time/residue: 0.5838 time to fit residues: 162.4008 Evaluate side-chains 219 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 197 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 147 GLN C 244 ASN C 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.184725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138445 restraints weight = 17771.520| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.98 r_work: 0.3194 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16191 Z= 0.164 Angle : 0.578 10.301 22050 Z= 0.295 Chirality : 0.046 0.149 2376 Planarity : 0.005 0.050 2859 Dihedral : 5.001 94.181 2177 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.54 % Allowed : 11.44 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.19), residues: 1980 helix: -0.29 (0.61), residues: 81 sheet: 0.43 (0.18), residues: 867 loop : -0.05 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.014 0.001 TYR C 203 PHE 0.015 0.002 PHE G 24 TRP 0.011 0.001 TRP E 47 HIS 0.007 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00411 (16182) covalent geometry : angle 0.57423 (22032) SS BOND : bond 0.00680 ( 9) SS BOND : angle 2.27179 ( 18) hydrogen bonds : bond 0.03541 ( 419) hydrogen bonds : angle 4.89511 ( 1101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.558 Fit side-chains REVERT: A 128 MET cc_start: 0.8360 (tpp) cc_final: 0.8142 (tpt) REVERT: A 133 GLN cc_start: 0.7725 (mm110) cc_final: 0.7364 (mm-40) REVERT: A 147 GLN cc_start: 0.8078 (mt0) cc_final: 0.7678 (mt0) REVERT: A 151 GLU cc_start: 0.8120 (tp30) cc_final: 0.7869 (tp30) REVERT: A 305 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: A 478 ASP cc_start: 0.8411 (p0) cc_final: 0.8205 (p0) REVERT: A 479 GLN cc_start: 0.8177 (mp10) cc_final: 0.7743 (mm110) REVERT: A 509 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.6858 (pp30) REVERT: A 511 ARG cc_start: 0.7739 (mmp-170) cc_final: 0.6562 (mmp-170) REVERT: A 538 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7411 (mtmm) REVERT: A 611 ASP cc_start: 0.7995 (m-30) cc_final: 0.7724 (m-30) REVERT: A 612 THR cc_start: 0.8233 (m) cc_final: 0.7910 (t) REVERT: E 59 SER cc_start: 0.8470 (p) cc_final: 0.7963 (t) REVERT: G 5 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7092 (mp) REVERT: H 48 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7488 (tp) REVERT: B 90 LEU cc_start: 0.7844 (tt) cc_final: 0.7629 (tp) REVERT: B 391 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8371 (mp) REVERT: B 511 ARG cc_start: 0.7845 (mmp-170) cc_final: 0.7346 (tpp80) REVERT: B 512 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8178 (p0) REVERT: B 538 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7207 (mttm) REVERT: C 89 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7860 (mmtp) REVERT: C 128 MET cc_start: 0.8301 (tpp) cc_final: 0.8064 (tpp) REVERT: C 147 GLN cc_start: 0.8136 (mt0) cc_final: 0.7812 (mt0) REVERT: C 479 GLN cc_start: 0.8119 (mp10) cc_final: 0.7639 (mm110) REVERT: C 511 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7539 (tpp80) outliers start: 61 outliers final: 31 residues processed: 229 average time/residue: 0.5744 time to fit residues: 146.2947 Evaluate side-chains 209 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 483 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 179 optimal weight: 40.0000 chunk 42 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142311 restraints weight = 17645.827| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.40 r_work: 0.3139 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16191 Z= 0.138 Angle : 0.547 10.125 22050 Z= 0.279 Chirality : 0.046 0.145 2376 Planarity : 0.005 0.044 2859 Dihedral : 4.447 18.668 2175 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.76 % Allowed : 11.85 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.19), residues: 1980 helix: -0.13 (0.61), residues: 81 sheet: 0.48 (0.17), residues: 867 loop : -0.04 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 74 TYR 0.016 0.001 TYR C 203 PHE 0.012 0.001 PHE G 24 TRP 0.009 0.001 TRP A 336 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00346 (16182) covalent geometry : angle 0.54458 (22032) SS BOND : bond 0.00505 ( 9) SS BOND : angle 1.89272 ( 18) hydrogen bonds : bond 0.02896 ( 419) hydrogen bonds : angle 4.75473 ( 1101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 184 time to evaluate : 0.493 Fit side-chains REVERT: A 133 GLN cc_start: 0.7843 (mm110) cc_final: 0.7482 (mm-40) REVERT: A 147 GLN cc_start: 0.8143 (mt0) cc_final: 0.7768 (mt0) REVERT: A 189 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7752 (tt0) REVERT: A 244 ASN cc_start: 0.7861 (p0) cc_final: 0.7633 (p0) REVERT: A 305 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: A 478 ASP cc_start: 0.8596 (p0) cc_final: 0.8374 (p0) REVERT: A 479 GLN cc_start: 0.8335 (mp10) cc_final: 0.7889 (mm110) REVERT: A 509 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.6933 (pp30) REVERT: A 538 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7553 (mtmm) REVERT: A 611 ASP cc_start: 0.8139 (m-30) cc_final: 0.7886 (m-30) REVERT: E 59 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8151 (t) REVERT: G 88 TYR cc_start: 0.7833 (m-80) cc_final: 0.7628 (m-80) REVERT: H 60 VAL cc_start: 0.8084 (t) cc_final: 0.7790 (p) REVERT: B 90 LEU cc_start: 0.8002 (tt) cc_final: 0.7731 (tp) REVERT: B 147 GLN cc_start: 0.8108 (mt0) cc_final: 0.7759 (mt0) REVERT: B 350 ILE cc_start: 0.1541 (OUTLIER) cc_final: 0.1046 (pp) REVERT: B 391 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 509 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.6647 (pp30) REVERT: B 511 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7023 (tpp80) REVERT: B 512 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8132 (p0) REVERT: B 538 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7186 (mttm) REVERT: B 539 ASN cc_start: 0.8196 (m-40) cc_final: 0.7742 (m-40) REVERT: C 89 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7910 (mmtm) REVERT: C 128 MET cc_start: 0.8423 (tpp) cc_final: 0.8157 (tpp) REVERT: C 147 GLN cc_start: 0.8191 (mt0) cc_final: 0.7892 (mt0) REVERT: C 391 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8686 (mp) REVERT: C 477 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8352 (m) REVERT: C 479 GLN cc_start: 0.8269 (mp10) cc_final: 0.7835 (mm110) REVERT: C 483 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8672 (tm-30) REVERT: C 511 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7645 (mmp-170) REVERT: C 623 LEU cc_start: 0.8167 (tp) cc_final: 0.7937 (tt) outliers start: 82 outliers final: 43 residues processed: 244 average time/residue: 0.5674 time to fit residues: 154.6200 Evaluate side-chains 233 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 194 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN H 40 GLN B 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.179586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123862 restraints weight = 17677.677| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.35 r_work: 0.3073 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 16191 Z= 0.382 Angle : 0.770 11.770 22050 Z= 0.399 Chirality : 0.054 0.204 2376 Planarity : 0.007 0.079 2859 Dihedral : 5.238 21.971 2175 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.70 % Allowed : 13.82 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.19), residues: 1980 helix: -0.72 (0.57), residues: 81 sheet: 0.28 (0.17), residues: 918 loop : -0.28 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 74 TYR 0.019 0.003 TYR A 561 PHE 0.018 0.003 PHE I 24 TRP 0.018 0.003 TRP A 474 HIS 0.008 0.002 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00971 (16182) covalent geometry : angle 0.76575 (22032) SS BOND : bond 0.00723 ( 9) SS BOND : angle 2.82930 ( 18) hydrogen bonds : bond 0.04512 ( 419) hydrogen bonds : angle 5.23348 ( 1101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 0.578 Fit side-chains REVERT: A 133 GLN cc_start: 0.7781 (mm110) cc_final: 0.7462 (mm-40) REVERT: A 151 GLU cc_start: 0.8358 (tp30) cc_final: 0.8154 (tp30) REVERT: A 189 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7753 (tt0) REVERT: A 479 GLN cc_start: 0.8354 (mp10) cc_final: 0.7746 (mm110) REVERT: A 509 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.6980 (pp30) REVERT: A 538 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7303 (mtmm) REVERT: A 539 ASN cc_start: 0.8266 (m-40) cc_final: 0.7816 (m-40) REVERT: A 611 ASP cc_start: 0.8105 (m-30) cc_final: 0.7811 (m-30) REVERT: E 46 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: E 48 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8010 (mp) REVERT: E 59 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8208 (t) REVERT: F 103 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.6499 (mpt) REVERT: B 90 LEU cc_start: 0.7992 (tt) cc_final: 0.7725 (tp) REVERT: B 350 ILE cc_start: 0.1331 (OUTLIER) cc_final: 0.0801 (pp) REVERT: B 391 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8554 (mt) REVERT: B 509 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.6777 (pp30) REVERT: B 511 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6946 (mmp-170) REVERT: B 538 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7310 (mttm) REVERT: C 89 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7906 (mmtp) REVERT: C 128 MET cc_start: 0.8370 (tpp) cc_final: 0.8119 (mmm) REVERT: C 305 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6850 (t0) REVERT: C 391 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8764 (mp) REVERT: C 479 GLN cc_start: 0.8398 (mp10) cc_final: 0.7824 (mm110) REVERT: C 483 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: C 511 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7554 (mmp-170) outliers start: 81 outliers final: 53 residues processed: 236 average time/residue: 0.5723 time to fit residues: 150.7057 Evaluate side-chains 237 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 31 optimal weight: 0.9980 chunk 157 optimal weight: 0.3980 chunk 168 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN A 499 GLN C 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141666 restraints weight = 17562.640| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.37 r_work: 0.3103 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16191 Z= 0.104 Angle : 0.527 9.696 22050 Z= 0.270 Chirality : 0.044 0.138 2376 Planarity : 0.005 0.044 2859 Dihedral : 4.587 19.927 2175 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.60 % Allowed : 15.16 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.19), residues: 1980 helix: -0.24 (0.60), residues: 81 sheet: 0.40 (0.17), residues: 870 loop : -0.08 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 74 TYR 0.015 0.001 TYR C 203 PHE 0.008 0.001 PHE E 29 TRP 0.010 0.001 TRP E 47 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00254 (16182) covalent geometry : angle 0.52377 (22032) SS BOND : bond 0.00578 ( 9) SS BOND : angle 1.97867 ( 18) hydrogen bonds : bond 0.02699 ( 419) hydrogen bonds : angle 4.77753 ( 1101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 0.606 Fit side-chains REVERT: A 128 MET cc_start: 0.8241 (tpt) cc_final: 0.8003 (tpt) REVERT: A 133 GLN cc_start: 0.7705 (mm110) cc_final: 0.7419 (mm-40) REVERT: A 147 GLN cc_start: 0.8069 (mt0) cc_final: 0.7684 (mt0) REVERT: A 151 GLU cc_start: 0.8198 (tp30) cc_final: 0.7250 (tt0) REVERT: A 174 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7689 (mtp180) REVERT: A 189 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7729 (tt0) REVERT: A 305 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6557 (m-30) REVERT: A 479 GLN cc_start: 0.8395 (mp10) cc_final: 0.7854 (mm110) REVERT: A 509 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.6861 (pp30) REVERT: A 538 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7458 (mtmm) REVERT: A 611 ASP cc_start: 0.8011 (m-30) cc_final: 0.7747 (m-30) REVERT: E 59 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8141 (t) REVERT: F 46 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: G 21 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7881 (t) REVERT: G 105 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7071 (t) REVERT: H 60 VAL cc_start: 0.8006 (t) cc_final: 0.7687 (p) REVERT: I 21 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7883 (t) REVERT: B 90 LEU cc_start: 0.7935 (tt) cc_final: 0.7649 (tp) REVERT: B 147 GLN cc_start: 0.8079 (mt0) cc_final: 0.7690 (mt0) REVERT: B 350 ILE cc_start: 0.1537 (OUTLIER) cc_final: 0.1048 (pp) REVERT: B 391 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 509 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.6529 (pp30) REVERT: B 511 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6868 (mmp-170) REVERT: B 512 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 538 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7306 (mttm) REVERT: C 89 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7888 (mmtp) REVERT: C 128 MET cc_start: 0.8403 (tpp) cc_final: 0.8177 (tpp) REVERT: C 147 GLN cc_start: 0.8155 (mt0) cc_final: 0.7863 (mt0) REVERT: C 222 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8207 (p) REVERT: C 305 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6370 (t0) REVERT: C 479 GLN cc_start: 0.8407 (mp10) cc_final: 0.7783 (mm110) REVERT: C 511 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7625 (mmp-170) outliers start: 62 outliers final: 29 residues processed: 217 average time/residue: 0.5942 time to fit residues: 143.1943 Evaluate side-chains 210 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124565 restraints weight = 17519.541| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.45 r_work: 0.3080 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 16191 Z= 0.279 Angle : 0.668 10.895 22050 Z= 0.344 Chirality : 0.050 0.169 2376 Planarity : 0.006 0.057 2859 Dihedral : 4.986 21.015 2175 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.89 % Allowed : 16.20 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.19), residues: 1980 helix: -0.52 (0.58), residues: 81 sheet: 0.32 (0.17), residues: 903 loop : -0.17 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 307 TYR 0.017 0.002 TYR A 561 PHE 0.013 0.002 PHE G 24 TRP 0.016 0.002 TRP C 474 HIS 0.009 0.002 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00713 (16182) covalent geometry : angle 0.66446 (22032) SS BOND : bond 0.00587 ( 9) SS BOND : angle 2.39421 ( 18) hydrogen bonds : bond 0.03814 ( 419) hydrogen bonds : angle 4.98628 ( 1101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 168 time to evaluate : 0.626 Fit side-chains REVERT: A 133 GLN cc_start: 0.7757 (mm110) cc_final: 0.7446 (mm-40) REVERT: A 147 GLN cc_start: 0.8131 (mt0) cc_final: 0.7709 (mt0) REVERT: A 189 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7768 (tt0) REVERT: A 479 GLN cc_start: 0.8361 (mp10) cc_final: 0.7738 (mm110) REVERT: A 509 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.6942 (pp30) REVERT: A 538 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7386 (mtmm) REVERT: A 611 ASP cc_start: 0.8066 (m-30) cc_final: 0.7853 (m-30) REVERT: A 612 THR cc_start: 0.8413 (m) cc_final: 0.7970 (t) REVERT: E 59 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8202 (t) REVERT: G 21 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 90 LEU cc_start: 0.7895 (tt) cc_final: 0.7606 (tp) REVERT: B 350 ILE cc_start: 0.1248 (OUTLIER) cc_final: 0.0758 (pp) REVERT: B 391 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 498 MET cc_start: 0.8470 (mmm) cc_final: 0.8066 (mmm) REVERT: B 509 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.6740 (pp30) REVERT: B 511 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6880 (mmp-170) REVERT: B 538 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7298 (mttm) REVERT: C 89 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7871 (mmtp) REVERT: C 128 MET cc_start: 0.8364 (tpp) cc_final: 0.8154 (mmm) REVERT: C 147 GLN cc_start: 0.8235 (mt0) cc_final: 0.7944 (mt0) REVERT: C 174 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7789 (mtp180) REVERT: C 189 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7506 (tt0) REVERT: C 305 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6697 (t0) REVERT: C 391 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8736 (mp) REVERT: C 479 GLN cc_start: 0.8464 (mp10) cc_final: 0.7774 (mm110) REVERT: C 511 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7558 (mmp-170) outliers start: 67 outliers final: 42 residues processed: 221 average time/residue: 0.5660 time to fit residues: 139.6881 Evaluate side-chains 217 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 140 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 144 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141912 restraints weight = 17692.028| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.24 r_work: 0.3099 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16191 Z= 0.107 Angle : 0.527 9.491 22050 Z= 0.270 Chirality : 0.044 0.144 2376 Planarity : 0.005 0.042 2859 Dihedral : 4.539 19.630 2175 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.90 % Allowed : 17.31 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.19), residues: 1980 helix: -0.20 (0.60), residues: 81 sheet: 0.44 (0.17), residues: 852 loop : -0.04 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 74 TYR 0.014 0.001 TYR C 203 PHE 0.008 0.001 PHE F 29 TRP 0.009 0.001 TRP C 474 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00264 (16182) covalent geometry : angle 0.52442 (22032) SS BOND : bond 0.00424 ( 9) SS BOND : angle 1.98532 ( 18) hydrogen bonds : bond 0.02652 ( 419) hydrogen bonds : angle 4.68407 ( 1101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.619 Fit side-chains REVERT: A 133 GLN cc_start: 0.7686 (mm110) cc_final: 0.7400 (mm-40) REVERT: A 147 GLN cc_start: 0.8076 (mt0) cc_final: 0.7699 (mt0) REVERT: A 151 GLU cc_start: 0.8190 (tp30) cc_final: 0.7180 (tt0) REVERT: A 174 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7711 (mtp180) REVERT: A 189 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7709 (tt0) REVERT: A 479 GLN cc_start: 0.8405 (mp10) cc_final: 0.7864 (mm110) REVERT: A 509 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.6838 (pp30) REVERT: A 538 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7465 (mtmm) REVERT: A 611 ASP cc_start: 0.7973 (m-30) cc_final: 0.7706 (m-30) REVERT: E 59 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8131 (t) REVERT: G 21 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7901 (t) REVERT: G 105 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7171 (t) REVERT: H 60 VAL cc_start: 0.7940 (t) cc_final: 0.7612 (p) REVERT: I 21 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7869 (t) REVERT: B 90 LEU cc_start: 0.7866 (tt) cc_final: 0.7575 (tp) REVERT: B 350 ILE cc_start: 0.1239 (OUTLIER) cc_final: 0.0759 (pp) REVERT: B 391 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 498 MET cc_start: 0.8343 (mmm) cc_final: 0.7975 (mmm) REVERT: B 509 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.6541 (pp30) REVERT: B 511 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6845 (mmp-170) REVERT: B 512 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 538 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7294 (mttm) REVERT: C 89 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7897 (mmtp) REVERT: C 147 GLN cc_start: 0.8138 (mt0) cc_final: 0.7840 (mt0) REVERT: C 174 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7735 (mtp180) REVERT: C 189 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7615 (tp30) REVERT: C 202 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7531 (mt-10) REVERT: C 222 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8184 (p) REVERT: C 391 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8583 (mp) REVERT: C 479 GLN cc_start: 0.8564 (mp10) cc_final: 0.7783 (mm110) REVERT: C 511 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7611 (mmp-170) outliers start: 50 outliers final: 29 residues processed: 216 average time/residue: 0.5909 time to fit residues: 141.5190 Evaluate side-chains 205 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.0050 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126059 restraints weight = 17642.333| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.42 r_work: 0.3131 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16191 Z= 0.114 Angle : 0.522 8.757 22050 Z= 0.267 Chirality : 0.045 0.141 2376 Planarity : 0.004 0.042 2859 Dihedral : 4.385 18.920 2175 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.14 % Allowed : 17.71 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 1980 helix: -0.04 (0.60), residues: 81 sheet: 0.50 (0.17), residues: 873 loop : 0.07 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 74 TYR 0.013 0.001 TYR C 203 PHE 0.007 0.001 PHE C 161 TRP 0.010 0.001 TRP C 474 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00287 (16182) covalent geometry : angle 0.51939 (22032) SS BOND : bond 0.00359 ( 9) SS BOND : angle 1.94558 ( 18) hydrogen bonds : bond 0.02620 ( 419) hydrogen bonds : angle 4.56137 ( 1101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.596 Fit side-chains REVERT: A 133 GLN cc_start: 0.7798 (mm110) cc_final: 0.7471 (mm-40) REVERT: A 147 GLN cc_start: 0.7972 (mt0) cc_final: 0.7559 (mt0) REVERT: A 151 GLU cc_start: 0.8275 (tp30) cc_final: 0.7255 (tt0) REVERT: A 174 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7767 (mtp180) REVERT: A 189 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7762 (tt0) REVERT: A 479 GLN cc_start: 0.8352 (mp10) cc_final: 0.7794 (mm110) REVERT: A 509 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.6784 (pp30) REVERT: A 538 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7404 (mtmm) REVERT: A 611 ASP cc_start: 0.7970 (m-30) cc_final: 0.7690 (m-30) REVERT: D 38 ARG cc_start: 0.8182 (ptt180) cc_final: 0.7979 (ptt180) REVERT: E 59 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8174 (t) REVERT: G 21 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7872 (t) REVERT: G 105 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7245 (t) REVERT: H 60 VAL cc_start: 0.7748 (t) cc_final: 0.7424 (p) REVERT: I 21 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7843 (t) REVERT: B 90 LEU cc_start: 0.7858 (tt) cc_final: 0.7529 (tp) REVERT: B 244 ASN cc_start: 0.7821 (p0) cc_final: 0.7212 (p0) REVERT: B 350 ILE cc_start: 0.1297 (OUTLIER) cc_final: 0.0824 (pp) REVERT: B 391 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8384 (mt) REVERT: B 498 MET cc_start: 0.8340 (mmm) cc_final: 0.7875 (mmm) REVERT: B 509 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.6505 (pp30) REVERT: B 511 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6928 (tpp80) REVERT: B 512 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8077 (p0) REVERT: B 538 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7266 (mttm) REVERT: C 89 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7874 (mmtp) REVERT: C 147 GLN cc_start: 0.8198 (mt0) cc_final: 0.7728 (mp10) REVERT: C 174 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7740 (mtp180) REVERT: C 189 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7591 (tp30) REVERT: C 202 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7653 (mt-10) REVERT: C 222 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 391 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 479 GLN cc_start: 0.8546 (mp10) cc_final: 0.7711 (mm110) REVERT: C 511 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7573 (mmp-170) outliers start: 54 outliers final: 34 residues processed: 212 average time/residue: 0.5965 time to fit residues: 140.5243 Evaluate side-chains 212 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 509 GLN Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 606 PHE Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 GLN C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.185275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144664 restraints weight = 17571.001| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.09 r_work: 0.3161 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16191 Z= 0.089 Angle : 0.491 7.955 22050 Z= 0.250 Chirality : 0.044 0.138 2376 Planarity : 0.004 0.042 2859 Dihedral : 4.152 18.254 2175 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.56 % Allowed : 18.58 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 1980 helix: 0.17 (0.61), residues: 81 sheet: 0.58 (0.18), residues: 846 loop : 0.20 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 74 TYR 0.014 0.001 TYR C 203 PHE 0.007 0.001 PHE A 92 TRP 0.007 0.001 TRP C 474 HIS 0.004 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00221 (16182) covalent geometry : angle 0.48868 (22032) SS BOND : bond 0.00334 ( 9) SS BOND : angle 1.63910 ( 18) hydrogen bonds : bond 0.02319 ( 419) hydrogen bonds : angle 4.40011 ( 1101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.611 Fit side-chains REVERT: A 75 ASN cc_start: 0.8005 (p0) cc_final: 0.7228 (p0) REVERT: A 133 GLN cc_start: 0.7890 (mm110) cc_final: 0.7560 (mm-40) REVERT: A 147 GLN cc_start: 0.7967 (mt0) cc_final: 0.7624 (mt0) REVERT: A 151 GLU cc_start: 0.8231 (tp30) cc_final: 0.7953 (mm-30) REVERT: A 189 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7819 (tt0) REVERT: A 479 GLN cc_start: 0.8406 (mp10) cc_final: 0.7888 (mm110) REVERT: A 509 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.6922 (pp30) REVERT: A 538 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7545 (mtmm) REVERT: A 611 ASP cc_start: 0.8072 (m-30) cc_final: 0.7813 (m-30) REVERT: E 59 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8215 (t) REVERT: G 21 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7932 (t) REVERT: H 60 VAL cc_start: 0.7790 (t) cc_final: 0.7541 (p) REVERT: I 21 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7837 (t) REVERT: B 90 LEU cc_start: 0.7937 (tt) cc_final: 0.7600 (tp) REVERT: B 244 ASN cc_start: 0.7827 (p0) cc_final: 0.7324 (p0) REVERT: B 350 ILE cc_start: 0.1477 (OUTLIER) cc_final: 0.1003 (pp) REVERT: B 391 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 498 MET cc_start: 0.8327 (mmm) cc_final: 0.7904 (mmm) REVERT: B 511 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7346 (tpp80) REVERT: B 538 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7387 (mttm) REVERT: C 89 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7925 (mmtp) REVERT: C 147 GLN cc_start: 0.8130 (mt0) cc_final: 0.7847 (mt0) REVERT: C 202 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7751 (mt-10) REVERT: C 222 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8179 (p) REVERT: C 391 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8593 (mp) REVERT: C 479 GLN cc_start: 0.8572 (mp10) cc_final: 0.7795 (mm110) REVERT: C 511 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7669 (mmp-170) outliers start: 44 outliers final: 27 residues processed: 210 average time/residue: 0.5873 time to fit residues: 137.2221 Evaluate side-chains 207 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 511 ARG Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 606 PHE Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 44 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 157 optimal weight: 0.0470 chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 GLN C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130288 restraints weight = 17566.634| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.35 r_work: 0.3199 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16191 Z= 0.090 Angle : 0.491 8.030 22050 Z= 0.250 Chirality : 0.044 0.137 2376 Planarity : 0.004 0.042 2859 Dihedral : 4.055 18.263 2175 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 1980 helix: 0.21 (0.61), residues: 81 sheet: 0.62 (0.18), residues: 849 loop : 0.30 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 74 TYR 0.013 0.001 TYR C 203 PHE 0.007 0.001 PHE A 92 TRP 0.007 0.001 TRP B 474 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00223 (16182) covalent geometry : angle 0.48888 (22032) SS BOND : bond 0.00297 ( 9) SS BOND : angle 1.62145 ( 18) hydrogen bonds : bond 0.02322 ( 419) hydrogen bonds : angle 4.34995 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5438.23 seconds wall clock time: 93 minutes 20.19 seconds (5600.19 seconds total)