Starting phenix.real_space_refine on Sat Jun 14 02:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3q_38895/06_2025/8y3q_38895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3q_38895/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3q_38895/06_2025/8y3q_38895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3q_38895/06_2025/8y3q_38895.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3q_38895/06_2025/8y3q_38895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3q_38895/06_2025/8y3q_38895.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.130 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.18, per 1000 atoms: 0.65 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: 3.70 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.14 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: 5.23 Time building geometry restraints manager: 4.44 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: 1.090 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.960 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS A 80 PHE 0.020 0.001 PHE C 92 TYR 0.015 0.001 TYR C 74 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.18926 ( 419) hydrogen bonds : angle 5.97569 ( 1101) SS BOND : bond 0.00494 ( 9) SS BOND : angle 2.03470 ( 18) covalent geometry : bond 0.00313 (16182) covalent geometry : angle 0.54801 (22032) *********************** 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 : 1.685 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: 1.1756 time to fit residues: 375.1860 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 : 2.093 ------------------------------------------------------------------------------- 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 169 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 52 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 chunk 157 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 499 GLN A 502 HIS G 6 GLN H 6 GLN H 33 ASN H 40 GLN I 33 ASN B 244 ASN B 502 HIS C 147 GLN C 246 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.192572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152432 restraints weight = 17951.723| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.34 r_work: 0.3271 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16191 Z= 0.096 Angle : 0.520 7.988 22050 Z= 0.268 Chirality : 0.044 0.142 2376 Planarity : 0.005 0.050 2859 Dihedral : 4.321 26.579 2177 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.73 % Allowed : 7.38 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1980 helix: -0.15 (0.63), residues: 81 sheet: 0.48 (0.18), residues: 837 loop : -0.01 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 47 HIS 0.005 0.001 HIS B 80 PHE 0.016 0.001 PHE A 92 TYR 0.023 0.001 TYR C 203 ARG 0.004 0.000 ARG C 192 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 419) hydrogen bonds : angle 4.90858 ( 1101) SS BOND : bond 0.00663 ( 9) SS BOND : angle 1.73006 ( 18) covalent geometry : bond 0.00224 (16182) covalent geometry : angle 0.51791 (22032) *********************** 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 246 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 2.362 Fit side-chains REVERT: A 133 GLN cc_start: 0.7754 (mm110) cc_final: 0.7377 (mm-40) REVERT: A 202 GLU cc_start: 0.7887 (tt0) cc_final: 0.7653 (tm-30) REVERT: A 305 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6507 (m-30) REVERT: A 479 GLN cc_start: 0.8078 (mp10) cc_final: 0.7762 (mm110) REVERT: A 534 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8150 (mt) REVERT: A 538 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7397 (mtmm) REVERT: A 539 ASN cc_start: 0.8204 (m-40) cc_final: 0.7752 (m-40) REVERT: A 611 ASP cc_start: 0.8176 (m-30) cc_final: 0.7931 (m-30) REVERT: A 612 THR cc_start: 0.8338 (m) cc_final: 0.7929 (t) REVERT: D 54 ASP cc_start: 0.8026 (m-30) cc_final: 0.7809 (m-30) REVERT: F 46 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7862 (tt0) REVERT: G 77 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7152 (mp) REVERT: G 88 TYR cc_start: 0.7702 (m-80) cc_final: 0.7423 (m-80) REVERT: I 77 ILE cc_start: 0.7747 (mt) cc_final: 0.7491 (mp) REVERT: B 89 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8175 (mmmt) REVERT: B 163 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7981 (mtp180) REVERT: B 538 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7055 (mttm) REVERT: B 539 ASN cc_start: 0.8119 (m-40) cc_final: 0.7797 (m-40) REVERT: C 128 MET cc_start: 0.8304 (tpp) cc_final: 0.8045 (tpp) REVERT: C 235 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8049 (tt0) REVERT: C 333 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7043 (mm) REVERT: C 479 GLN cc_start: 0.8028 (mp10) cc_final: 0.7578 (mm110) REVERT: C 541 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7228 (t) outliers start: 47 outliers final: 28 residues processed: 227 average time/residue: 1.1397 time to fit residues: 290.3295 Evaluate side-chains 212 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 477 SER Chi-restraints excluded: chain A residue 534 LEU 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 98 CYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 77 ILE 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 232 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 622 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 305 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 483 GLN 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 179 optimal weight: 30.0000 chunk 137 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 0.0170 chunk 85 optimal weight: 6.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- 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** I 40 GLN B 88 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 147 GLN C 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141554 restraints weight = 17491.858| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.38 r_work: 0.3128 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16191 Z= 0.237 Angle : 0.646 11.233 22050 Z= 0.331 Chirality : 0.049 0.161 2376 Planarity : 0.005 0.052 2859 Dihedral : 5.222 99.171 2177 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.89 % Allowed : 10.34 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1980 helix: -0.14 (0.62), residues: 78 sheet: 0.42 (0.18), residues: 867 loop : -0.10 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 47 HIS 0.005 0.002 HIS B 102 PHE 0.018 0.002 PHE G 24 TYR 0.017 0.002 TYR C 203 ARG 0.004 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 419) hydrogen bonds : angle 5.02236 ( 1101) SS BOND : bond 0.00870 ( 9) SS BOND : angle 2.61634 ( 18) covalent geometry : bond 0.00610 (16182) covalent geometry : angle 0.64160 (22032) *********************** 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 263 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 2.113 Fit side-chains REVERT: A 133 GLN cc_start: 0.7879 (mm110) cc_final: 0.7549 (mm-40) REVERT: A 305 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: A 478 ASP cc_start: 0.8493 (p0) cc_final: 0.8259 (p0) REVERT: A 479 GLN cc_start: 0.8293 (mp10) cc_final: 0.7887 (mm110) REVERT: A 498 MET cc_start: 0.8458 (mmm) cc_final: 0.8152 (mmm) REVERT: A 509 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.6676 (pp30) REVERT: A 538 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7590 (mtmm) REVERT: A 611 ASP cc_start: 0.8094 (m-30) cc_final: 0.7815 (m-30) REVERT: A 612 THR cc_start: 0.8343 (m) cc_final: 0.7970 (t) REVERT: G 88 TYR cc_start: 0.7860 (m-80) cc_final: 0.7655 (m-80) REVERT: H 48 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7587 (tp) REVERT: I 10 MET cc_start: 0.7063 (tpp) cc_final: 0.6859 (tpp) REVERT: B 90 LEU cc_start: 0.7914 (tt) cc_final: 0.7672 (tp) REVERT: B 391 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8467 (mt) REVERT: B 509 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.6826 (pp30) REVERT: B 538 LYS cc_start: 0.7810 (mtpt) cc_final: 0.7143 (mttm) REVERT: B 539 ASN cc_start: 0.8232 (m-40) cc_final: 0.7794 (m-40) REVERT: C 128 MET cc_start: 0.8325 (tpp) cc_final: 0.7980 (mmm) REVERT: C 479 GLN cc_start: 0.8132 (mp10) cc_final: 0.7705 (mm110) REVERT: C 511 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7622 (tpp80) outliers start: 67 outliers final: 36 residues processed: 241 average time/residue: 1.2280 time to fit residues: 330.7742 Evaluate side-chains 213 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 623 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 59 SER 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 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 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 I residue 105 THR 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 509 GLN 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 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 483 GLN Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 105 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.185164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143138 restraints weight = 17588.080| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.39 r_work: 0.3154 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2438 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= 0.123 Angle : 0.532 10.173 22050 Z= 0.271 Chirality : 0.045 0.144 2376 Planarity : 0.005 0.045 2859 Dihedral : 4.471 18.728 2175 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.54 % Allowed : 12.89 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1980 helix: -0.12 (0.61), residues: 81 sheet: 0.50 (0.18), residues: 867 loop : -0.04 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.007 0.001 HIS A 114 PHE 0.010 0.001 PHE G 24 TYR 0.016 0.001 TYR C 203 ARG 0.003 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02898 ( 419) hydrogen bonds : angle 4.75765 ( 1101) SS BOND : bond 0.00522 ( 9) SS BOND : angle 1.85997 ( 18) covalent geometry : bond 0.00309 (16182) covalent geometry : angle 0.52967 (22032) *********************** 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 243 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 1.838 Fit side-chains REVERT: A 128 MET cc_start: 0.8463 (tpp) cc_final: 0.8234 (tpt) REVERT: A 133 GLN cc_start: 0.7835 (mm110) cc_final: 0.7467 (mm-40) REVERT: A 147 GLN cc_start: 0.8146 (mt0) cc_final: 0.7775 (mt0) REVERT: A 151 GLU cc_start: 0.8242 (tp30) cc_final: 0.7285 (tt0) REVERT: A 244 ASN cc_start: 0.7800 (p0) cc_final: 0.7579 (p0) REVERT: A 305 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: A 478 ASP cc_start: 0.8508 (p0) cc_final: 0.8303 (p0) REVERT: A 479 GLN cc_start: 0.8270 (mp10) cc_final: 0.7846 (mm110) REVERT: A 509 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.6599 (pp30) REVERT: A 538 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7462 (mtmm) REVERT: A 539 ASN cc_start: 0.8293 (m110) cc_final: 0.7951 (m-40) REVERT: A 611 ASP cc_start: 0.8048 (m-30) cc_final: 0.7780 (m-30) REVERT: A 612 THR cc_start: 0.8255 (m) cc_final: 0.7893 (t) REVERT: A 613 ASP cc_start: 0.7525 (t0) cc_final: 0.7320 (t0) REVERT: D 46 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: E 59 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8091 (t) REVERT: G 5 ILE cc_start: 0.7394 (pt) cc_final: 0.7168 (mp) REVERT: B 90 LEU cc_start: 0.7944 (tt) cc_final: 0.7676 (tp) REVERT: B 350 ILE cc_start: 0.1307 (OUTLIER) cc_final: 0.0799 (pp) REVERT: B 498 MET cc_start: 0.8466 (mmm) cc_final: 0.8156 (mmm) REVERT: B 509 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.6602 (pp30) REVERT: B 511 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7053 (tpp80) REVERT: B 512 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8141 (p0) REVERT: B 538 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7172 (mttm) REVERT: B 539 ASN cc_start: 0.8197 (m-40) cc_final: 0.7744 (m-40) REVERT: C 128 MET cc_start: 0.8422 (tpp) cc_final: 0.8091 (mmm) REVERT: C 147 GLN cc_start: 0.8246 (mt0) cc_final: 0.7969 (mt0) REVERT: C 360 LYS cc_start: 0.8356 (tmtt) cc_final: 0.8138 (tmtt) REVERT: C 479 GLN cc_start: 0.8203 (mp10) cc_final: 0.7717 (mm110) REVERT: C 483 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: C 511 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7614 (tpp80) outliers start: 61 outliers final: 33 residues processed: 227 average time/residue: 1.3933 time to fit residues: 353.8636 Evaluate side-chains 213 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 623 LEU Chi-restraints excluded: chain D residue 46 GLU 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 F residue 73 SER 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 105 THR Chi-restraints excluded: chain B residue 113 CYS 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 509 GLN 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 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 483 GLN Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 613 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 140 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 0.0030 chunk 198 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128706 restraints weight = 17802.625| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.57 r_work: 0.3206 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16191 Z= 0.186 Angle : 0.591 10.768 22050 Z= 0.304 Chirality : 0.047 0.150 2376 Planarity : 0.005 0.044 2859 Dihedral : 4.646 19.268 2175 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.59 % Allowed : 13.01 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1980 helix: -0.26 (0.60), residues: 81 sheet: 0.47 (0.17), residues: 867 loop : -0.06 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 474 HIS 0.006 0.001 HIS A 114 PHE 0.014 0.002 PHE G 24 TYR 0.014 0.002 TYR A 561 ARG 0.004 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 419) hydrogen bonds : angle 4.83706 ( 1101) SS BOND : bond 0.00618 ( 9) SS BOND : angle 2.10824 ( 18) covalent geometry : bond 0.00471 (16182) covalent geometry : angle 0.58846 (22032) *********************** 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 260 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 181 time to evaluate : 1.536 Fit side-chains REVERT: A 133 GLN cc_start: 0.7784 (mm110) cc_final: 0.7415 (mm-40) REVERT: A 147 GLN cc_start: 0.8123 (mt0) cc_final: 0.7696 (mt0) REVERT: A 151 GLU cc_start: 0.8283 (tp30) cc_final: 0.8069 (tp30) REVERT: A 189 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7723 (tt0) REVERT: A 244 ASN cc_start: 0.7689 (p0) cc_final: 0.7421 (p0) REVERT: A 305 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: A 479 GLN cc_start: 0.8293 (mp10) cc_final: 0.7762 (mm110) REVERT: A 509 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.6923 (pp30) REVERT: A 538 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7361 (mtmm) REVERT: A 611 ASP cc_start: 0.8057 (m-30) cc_final: 0.7801 (m-30) REVERT: A 612 THR cc_start: 0.8258 (m) cc_final: 0.7925 (t) REVERT: D 46 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: E 59 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8146 (t) REVERT: G 21 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7775 (t) REVERT: I 10 MET cc_start: 0.7337 (tpp) cc_final: 0.7044 (tpp) REVERT: B 90 LEU cc_start: 0.7931 (tt) cc_final: 0.7644 (tp) REVERT: B 350 ILE cc_start: 0.1233 (OUTLIER) cc_final: 0.0776 (pp) REVERT: B 391 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 498 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8137 (mmm) REVERT: B 509 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.6607 (pp30) REVERT: B 512 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8153 (p0) REVERT: B 538 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7218 (mttm) REVERT: C 128 MET cc_start: 0.8408 (tpp) cc_final: 0.8198 (tpp) REVERT: C 147 GLN cc_start: 0.8273 (mt0) cc_final: 0.7981 (mt0) REVERT: C 391 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 477 SER cc_start: 0.8657 (t) cc_final: 0.8352 (m) REVERT: C 479 GLN cc_start: 0.8298 (mp10) cc_final: 0.7848 (mm110) REVERT: C 483 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: C 511 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7470 (tpp80) REVERT: C 611 ASP cc_start: 0.8035 (m-30) cc_final: 0.7770 (m-30) outliers start: 79 outliers final: 43 residues processed: 235 average time/residue: 1.1430 time to fit residues: 303.7585 Evaluate side-chains 226 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 A residue 623 LEU Chi-restraints excluded: chain D residue 46 GLU 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 7 SER 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 H residue 21 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 105 THR 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 498 MET Chi-restraints excluded: chain B residue 509 GLN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141305 restraints weight = 17635.701| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.35 r_work: 0.3076 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2931 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= 0.136 Angle : 0.539 9.784 22050 Z= 0.276 Chirality : 0.045 0.143 2376 Planarity : 0.005 0.043 2859 Dihedral : 4.484 18.976 2175 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.77 % Allowed : 14.63 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1980 helix: -0.19 (0.60), residues: 81 sheet: 0.49 (0.17), residues: 870 loop : 0.01 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.005 0.001 HIS A 114 PHE 0.009 0.001 PHE I 24 TYR 0.013 0.001 TYR C 203 ARG 0.003 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02836 ( 419) hydrogen bonds : angle 4.70688 ( 1101) SS BOND : bond 0.00364 ( 9) SS BOND : angle 1.78207 ( 18) covalent geometry : bond 0.00344 (16182) covalent geometry : angle 0.53700 (22032) *********************** 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 240 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 1.732 Fit side-chains REVERT: A 133 GLN cc_start: 0.7700 (mm110) cc_final: 0.7386 (mm-40) REVERT: A 147 GLN cc_start: 0.8054 (mt0) cc_final: 0.7669 (mt0) REVERT: A 151 GLU cc_start: 0.8179 (tp30) cc_final: 0.7970 (tp30) REVERT: A 189 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7651 (tt0) REVERT: A 244 ASN cc_start: 0.7747 (p0) cc_final: 0.7467 (p0) REVERT: A 305 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6472 (m-30) REVERT: A 479 GLN cc_start: 0.8377 (mp10) cc_final: 0.7853 (mm110) REVERT: A 509 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.6847 (pp30) REVERT: A 538 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7358 (mtmm) REVERT: A 611 ASP cc_start: 0.8013 (m-30) cc_final: 0.7777 (m-30) REVERT: A 612 THR cc_start: 0.8323 (m) cc_final: 0.7859 (t) REVERT: D 46 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: E 46 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: E 59 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8101 (t) REVERT: G 21 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7790 (t) REVERT: B 90 LEU cc_start: 0.7930 (tt) cc_final: 0.7624 (tp) REVERT: B 350 ILE cc_start: 0.1239 (OUTLIER) cc_final: 0.0778 (pp) REVERT: B 391 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 498 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8074 (mmm) REVERT: B 512 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8366 (p0) REVERT: B 538 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7223 (mttm) REVERT: C 128 MET cc_start: 0.8375 (tpp) cc_final: 0.8134 (tpp) REVERT: C 147 GLN cc_start: 0.8263 (mt0) cc_final: 0.8002 (mt0) REVERT: C 202 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7529 (mt-10) REVERT: C 305 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6372 (t0) REVERT: C 391 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8647 (mp) REVERT: C 477 SER cc_start: 0.8657 (t) cc_final: 0.8348 (m) REVERT: C 479 GLN cc_start: 0.8240 (mp10) cc_final: 0.7763 (mm110) REVERT: C 511 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7531 (tpp80) outliers start: 65 outliers final: 38 residues processed: 222 average time/residue: 1.1238 time to fit residues: 279.2640 Evaluate side-chains 220 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 219 ASP 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 46 GLU 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 46 GLU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 LEU 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 I residue 32 SER Chi-restraints excluded: chain I residue 105 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 483 GLN Chi-restraints excluded: chain B residue 498 MET 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 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 414 ILE 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 37 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.185625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143924 restraints weight = 17723.532| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.38 r_work: 0.3123 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2988 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= 0.095 Angle : 0.500 8.927 22050 Z= 0.255 Chirality : 0.044 0.137 2376 Planarity : 0.004 0.043 2859 Dihedral : 4.229 18.253 2175 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.02 % Allowed : 15.39 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1980 helix: 0.00 (0.61), residues: 81 sheet: 0.58 (0.18), residues: 837 loop : 0.13 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.006 0.001 HIS A 246 PHE 0.007 0.001 PHE D 70 TYR 0.014 0.001 TYR C 203 ARG 0.003 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02456 ( 419) hydrogen bonds : angle 4.54508 ( 1101) SS BOND : bond 0.00315 ( 9) SS BOND : angle 1.75373 ( 18) covalent geometry : bond 0.00235 (16182) covalent geometry : angle 0.49748 (22032) *********************** 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 225 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 1.847 Fit side-chains REVERT: A 75 ASN cc_start: 0.8024 (p0) cc_final: 0.7635 (p0) REVERT: A 133 GLN cc_start: 0.7776 (mm110) cc_final: 0.7514 (mm-40) REVERT: A 147 GLN cc_start: 0.8018 (mt0) cc_final: 0.7647 (mt0) REVERT: A 151 GLU cc_start: 0.8259 (tp30) cc_final: 0.7326 (tt0) REVERT: A 189 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7734 (tt0) REVERT: A 244 ASN cc_start: 0.7765 (p0) cc_final: 0.7503 (p0) REVERT: A 305 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: A 479 GLN cc_start: 0.8431 (mp10) cc_final: 0.7943 (mm110) REVERT: A 509 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.6902 (pp30) REVERT: A 538 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7505 (mtmm) REVERT: A 611 ASP cc_start: 0.8083 (m-30) cc_final: 0.7845 (m-30) REVERT: D 46 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: E 59 SER cc_start: 0.8685 (p) cc_final: 0.8202 (t) REVERT: G 21 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7850 (t) REVERT: H 98 ASP cc_start: 0.7292 (p0) cc_final: 0.7043 (p0) REVERT: B 90 LEU cc_start: 0.8001 (tt) cc_final: 0.7660 (tp) REVERT: B 244 ASN cc_start: 0.8038 (p0) cc_final: 0.7452 (p0) REVERT: B 350 ILE cc_start: 0.1542 (OUTLIER) cc_final: 0.1067 (pp) REVERT: B 391 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8355 (mp) REVERT: B 498 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: B 511 ARG cc_start: 0.7819 (mmp-170) cc_final: 0.7401 (tpp80) REVERT: B 538 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7367 (mttm) REVERT: C 128 MET cc_start: 0.8481 (tpp) cc_final: 0.8244 (tpp) REVERT: C 147 GLN cc_start: 0.8242 (mt0) cc_final: 0.7935 (mp10) REVERT: C 202 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7635 (mt-10) REVERT: C 222 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8188 (p) REVERT: C 391 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 477 SER cc_start: 0.8703 (t) cc_final: 0.8413 (m) REVERT: C 479 GLN cc_start: 0.8265 (mp10) cc_final: 0.7823 (mm110) REVERT: C 511 ARG cc_start: 0.8056 (mmm-85) cc_final: 0.7598 (tpp80) REVERT: C 623 LEU cc_start: 0.8073 (tp) cc_final: 0.7855 (tt) outliers start: 52 outliers final: 33 residues processed: 213 average time/residue: 1.6687 time to fit residues: 395.8191 Evaluate side-chains 206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 GLU 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 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 I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain B residue 113 CYS 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 498 MET Chi-restraints excluded: chain B residue 505 GLU 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 333 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 581 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 B 483 GLN C 416 ASN C 483 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138589 restraints weight = 17554.406| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.29 r_work: 0.3079 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 16191 Z= 0.325 Angle : 0.711 10.548 22050 Z= 0.367 Chirality : 0.052 0.176 2376 Planarity : 0.006 0.071 2859 Dihedral : 4.969 21.258 2175 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.07 % Allowed : 15.27 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1980 helix: -0.55 (0.58), residues: 81 sheet: 0.38 (0.17), residues: 942 loop : -0.11 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 474 HIS 0.008 0.002 HIS A 311 PHE 0.017 0.002 PHE G 24 TYR 0.019 0.002 TYR A 561 ARG 0.007 0.001 ARG C 174 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 419) hydrogen bonds : angle 4.99574 ( 1101) SS BOND : bond 0.00647 ( 9) SS BOND : angle 2.42591 ( 18) covalent geometry : bond 0.00828 (16182) covalent geometry : angle 0.70767 (22032) *********************** 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 238 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 168 time to evaluate : 1.885 Fit side-chains REVERT: A 133 GLN cc_start: 0.7867 (mm110) cc_final: 0.7586 (mm-40) REVERT: A 189 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7881 (tt0) REVERT: A 244 ASN cc_start: 0.8122 (p0) cc_final: 0.7873 (p0) REVERT: A 479 GLN cc_start: 0.8431 (mp10) cc_final: 0.7855 (mm110) REVERT: A 509 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7048 (pp30) REVERT: A 538 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7513 (mtmm) REVERT: A 611 ASP cc_start: 0.8145 (m-30) cc_final: 0.7887 (m-30) REVERT: D 46 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: E 59 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8262 (t) REVERT: G 21 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7839 (t) REVERT: H 98 ASP cc_start: 0.7477 (p0) cc_final: 0.7220 (p0) REVERT: I 105 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7189 (t) REVERT: B 90 LEU cc_start: 0.8048 (tt) cc_final: 0.7743 (tp) REVERT: B 163 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8119 (mtp180) REVERT: B 350 ILE cc_start: 0.1473 (OUTLIER) cc_final: 0.0990 (pp) REVERT: B 391 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 498 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: B 512 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8526 (p0) REVERT: B 538 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7425 (mttm) REVERT: C 128 MET cc_start: 0.8451 (tpp) cc_final: 0.8246 (tpp) REVERT: C 147 GLN cc_start: 0.8349 (mt0) cc_final: 0.8094 (mt0) REVERT: C 202 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7564 (mt-10) REVERT: C 391 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8796 (mp) REVERT: C 477 SER cc_start: 0.8641 (t) cc_final: 0.8398 (m) REVERT: C 479 GLN cc_start: 0.8346 (mp10) cc_final: 0.7888 (mm110) REVERT: C 511 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7564 (tpp80) outliers start: 70 outliers final: 43 residues processed: 222 average time/residue: 1.1284 time to fit residues: 280.2943 Evaluate side-chains 222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 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 D residue 46 GLU Chi-restraints excluded: chain D residue 59 SER 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 7 SER 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 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 I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 105 THR 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 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 498 MET Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 76 LYS 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 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 Chi-restraints excluded: chain C residue 581 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 483 GLN C 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140428 restraints weight = 17594.743| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.31 r_work: 0.3126 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16191 Z= 0.145 Angle : 0.559 9.408 22050 Z= 0.287 Chirality : 0.046 0.145 2376 Planarity : 0.005 0.042 2859 Dihedral : 4.609 20.313 2175 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.02 % Allowed : 16.38 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1980 helix: -0.25 (0.59), residues: 81 sheet: 0.48 (0.17), residues: 870 loop : -0.01 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 474 HIS 0.004 0.001 HIS A 114 PHE 0.009 0.001 PHE D 70 TYR 0.013 0.001 TYR C 203 ARG 0.004 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 419) hydrogen bonds : angle 4.76509 ( 1101) SS BOND : bond 0.00533 ( 9) SS BOND : angle 2.47715 ( 18) covalent geometry : bond 0.00367 (16182) covalent geometry : angle 0.55486 (22032) *********************** 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 218 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 1.695 Fit side-chains REVERT: A 133 GLN cc_start: 0.7830 (mm110) cc_final: 0.7490 (mm-40) REVERT: A 147 GLN cc_start: 0.8113 (mt0) cc_final: 0.7732 (mt0) REVERT: A 174 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: A 189 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7888 (tt0) REVERT: A 244 ASN cc_start: 0.7822 (p0) cc_final: 0.7565 (p0) REVERT: A 479 GLN cc_start: 0.8381 (mp10) cc_final: 0.7816 (mm110) REVERT: A 509 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.6945 (pp30) REVERT: A 538 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7459 (mtmm) REVERT: A 611 ASP cc_start: 0.7952 (m-30) cc_final: 0.7693 (m-30) REVERT: D 46 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: E 59 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8202 (t) REVERT: G 21 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7911 (t) REVERT: H 98 ASP cc_start: 0.7330 (p0) cc_final: 0.7092 (p0) REVERT: I 105 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7196 (t) REVERT: B 90 LEU cc_start: 0.7920 (tt) cc_final: 0.7620 (tp) REVERT: B 350 ILE cc_start: 0.1383 (OUTLIER) cc_final: 0.0941 (pp) REVERT: B 391 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8416 (mt) REVERT: B 498 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8205 (mmm) REVERT: B 538 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7398 (mttm) REVERT: C 128 MET cc_start: 0.8425 (tpp) cc_final: 0.8182 (tpp) REVERT: C 147 GLN cc_start: 0.8278 (mt0) cc_final: 0.7966 (mp10) REVERT: C 189 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7509 (tt0) REVERT: C 202 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7534 (mt-10) REVERT: C 391 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8645 (mp) REVERT: C 477 SER cc_start: 0.8650 (t) cc_final: 0.8413 (m) REVERT: C 479 GLN cc_start: 0.8349 (mp10) cc_final: 0.7842 (mm110) REVERT: C 511 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7569 (tpp80) outliers start: 52 outliers final: 37 residues processed: 209 average time/residue: 1.2057 time to fit residues: 282.2948 Evaluate side-chains 209 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 46 GLU 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 35 SER 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 I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 105 THR 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 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 498 MET Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 76 LYS 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 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 Chi-restraints excluded: chain C residue 581 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN H 33 ASN I 40 GLN B 483 GLN C 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.182187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137265 restraints weight = 17695.279| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.42 r_work: 0.3159 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3365 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= 0.151 Angle : 0.557 9.055 22050 Z= 0.284 Chirality : 0.046 0.145 2376 Planarity : 0.005 0.042 2859 Dihedral : 4.523 19.628 2175 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.43 % Allowed : 16.32 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1980 helix: -0.19 (0.59), residues: 81 sheet: 0.54 (0.17), residues: 852 loop : 0.05 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.006 0.001 HIS B 246 PHE 0.010 0.001 PHE G 24 TYR 0.013 0.001 TYR F 97 ARG 0.003 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 419) hydrogen bonds : angle 4.69215 ( 1101) SS BOND : bond 0.00493 ( 9) SS BOND : angle 2.28886 ( 18) covalent geometry : bond 0.00384 (16182) covalent geometry : angle 0.55297 (22032) ********************** 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 224 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 1.711 Fit side-chains REVERT: A 133 GLN cc_start: 0.7686 (mm110) cc_final: 0.7358 (mm-40) REVERT: A 147 GLN cc_start: 0.8064 (mt0) cc_final: 0.7723 (mt0) REVERT: A 151 GLU cc_start: 0.8207 (tp30) cc_final: 0.7245 (tt0) REVERT: A 174 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: A 189 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7791 (tt0) REVERT: A 244 ASN cc_start: 0.7728 (p0) cc_final: 0.7395 (p0) REVERT: A 479 GLN cc_start: 0.8347 (mp10) cc_final: 0.7779 (mm110) REVERT: A 509 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.6908 (pp30) REVERT: A 538 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7412 (mtmm) REVERT: A 611 ASP cc_start: 0.7885 (m-30) cc_final: 0.7621 (m-30) REVERT: E 59 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8163 (t) REVERT: G 21 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7906 (t) REVERT: I 98 ASP cc_start: 0.6897 (p0) cc_final: 0.6669 (p0) REVERT: I 105 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7230 (t) REVERT: B 90 LEU cc_start: 0.7893 (tt) cc_final: 0.7586 (tp) REVERT: B 350 ILE cc_start: 0.1232 (OUTLIER) cc_final: 0.0770 (pp) REVERT: B 391 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 498 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8104 (mmm) REVERT: B 511 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7296 (mmp-170) REVERT: B 538 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7337 (mttm) REVERT: C 128 MET cc_start: 0.8416 (tpp) cc_final: 0.8215 (tpp) REVERT: C 147 GLN cc_start: 0.8215 (mt0) cc_final: 0.7880 (mp10) REVERT: C 189 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7417 (tt0) REVERT: C 202 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7517 (mt-10) REVERT: C 391 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8644 (mp) REVERT: C 477 SER cc_start: 0.8618 (t) cc_final: 0.8368 (m) REVERT: C 479 GLN cc_start: 0.8305 (mp10) cc_final: 0.7829 (mm110) REVERT: C 511 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7558 (tpp80) outliers start: 59 outliers final: 42 residues processed: 212 average time/residue: 1.1533 time to fit residues: 273.2505 Evaluate side-chains 215 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 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 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 35 SER 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 106 LEU 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 I residue 32 SER Chi-restraints excluded: chain I residue 105 THR 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 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 498 MET 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 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 Chi-restraints excluded: chain C residue 581 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 54 optimal weight: 0.3980 chunk 110 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN B 483 GLN C 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141486 restraints weight = 17557.634| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.32 r_work: 0.3089 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16191 Z= 0.114 Angle : 0.525 8.545 22050 Z= 0.268 Chirality : 0.045 0.142 2376 Planarity : 0.004 0.042 2859 Dihedral : 4.343 18.654 2175 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.25 % Allowed : 16.55 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1980 helix: -0.06 (0.60), residues: 81 sheet: 0.58 (0.18), residues: 819 loop : 0.15 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 474 HIS 0.004 0.001 HIS A 114 PHE 0.007 0.001 PHE G 24 TYR 0.013 0.001 TYR C 203 ARG 0.003 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02642 ( 419) hydrogen bonds : angle 4.58132 ( 1101) SS BOND : bond 0.00398 ( 9) SS BOND : angle 2.01247 ( 18) covalent geometry : bond 0.00288 (16182) covalent geometry : angle 0.52169 (22032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10791.96 seconds wall clock time: 191 minutes 21.40 seconds (11481.40 seconds total)