Starting phenix.real_space_refine on Sun Oct 13 19:34:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3q_38895/10_2024/8y3q_38895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3q_38895/10_2024/8y3q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3q_38895/10_2024/8y3q_38895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3q_38895/10_2024/8y3q_38895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3q_38895/10_2024/8y3q_38895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3q_38895/10_2024/8y3q_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 9.22, per 1000 atoms: 0.59 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: 3.40 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: 2.57 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: 5.56 Time building geometry restraints manager: 4.01 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: 0.00 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: 1.100 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.560 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.530 ------------------------------------------------------------------------------- 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 16182 Z= 0.208 Angle : 0.548 7.159 22032 Z= 0.296 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.678 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: 1.1536 time to fit residues: 365.2772 Evaluate side-chains 188 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 16182 Z= 0.146 Angle : 0.518 7.988 22032 Z= 0.267 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 *********************** 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 fitting. rotamer outliers: 47 poor density : 199 time to evaluate : 1.867 Fit side-chains REVERT: A 133 GLN cc_start: 0.7211 (mm110) cc_final: 0.6848 (mm-40) REVERT: A 305 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5633 (m-30) REVERT: A 479 GLN cc_start: 0.7651 (mp10) cc_final: 0.7380 (mm110) REVERT: A 534 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7769 (mt) REVERT: A 538 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7150 (mtmm) REVERT: A 539 ASN cc_start: 0.7939 (m-40) cc_final: 0.7540 (m-40) REVERT: A 611 ASP cc_start: 0.7643 (m-30) cc_final: 0.7407 (m-30) REVERT: A 612 THR cc_start: 0.8193 (m) cc_final: 0.7836 (t) REVERT: D 54 ASP cc_start: 0.7520 (m-30) cc_final: 0.7294 (m-30) REVERT: F 46 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7469 (tt0) REVERT: G 77 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7455 (mp) REVERT: G 88 TYR cc_start: 0.7694 (m-80) cc_final: 0.7406 (m-80) REVERT: I 77 ILE cc_start: 0.7869 (mt) cc_final: 0.7666 (mp) REVERT: B 89 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7922 (mmmt) REVERT: B 163 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: B 538 LYS cc_start: 0.7245 (mtpt) cc_final: 0.6728 (mttm) REVERT: B 539 ASN cc_start: 0.7857 (m-40) cc_final: 0.7579 (m-40) REVERT: C 128 MET cc_start: 0.7938 (tpp) cc_final: 0.7682 (tpp) REVERT: C 235 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7608 (tt0) REVERT: C 388 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7409 (mtp180) REVERT: C 479 GLN cc_start: 0.7714 (mp10) cc_final: 0.7312 (mm110) REVERT: C 541 SER cc_start: 0.7603 (OUTLIER) cc_final: 0.7336 (t) outliers start: 47 outliers final: 28 residues processed: 227 average time/residue: 1.3569 time to fit residues: 343.3534 Evaluate side-chains 210 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 2.993 ------------------------------------------------------------------------------- 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 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 101 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 162 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 146 optimal weight: 4.9990 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN B 88 ASN B 416 ASN C 147 GLN C 244 ASN C 502 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16182 Z= 0.286 Angle : 0.599 11.239 22032 Z= 0.306 Chirality : 0.047 0.155 2376 Planarity : 0.005 0.051 2859 Dihedral : 5.023 93.131 2177 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.95 % Allowed : 10.10 % Favored : 85.95 % 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: -0.01 (0.63), residues: 78 sheet: 0.46 (0.18), residues: 867 loop : -0.02 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 47 HIS 0.005 0.001 HIS B 102 PHE 0.017 0.002 PHE G 24 TYR 0.017 0.002 TYR C 203 ARG 0.004 0.001 ARG A 192 *********************** 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 269 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 1.800 Fit side-chains REVERT: A 133 GLN cc_start: 0.7358 (mm110) cc_final: 0.7025 (mm-40) REVERT: A 147 GLN cc_start: 0.7609 (mt0) cc_final: 0.7235 (mt0) REVERT: A 305 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5622 (m-30) REVERT: A 479 GLN cc_start: 0.7829 (mp10) cc_final: 0.7485 (mm110) REVERT: A 509 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.6722 (pp30) REVERT: A 538 LYS cc_start: 0.7654 (mtpt) cc_final: 0.7314 (mtmm) REVERT: A 611 ASP cc_start: 0.7660 (m-30) cc_final: 0.7420 (m-30) REVERT: A 612 THR cc_start: 0.8221 (m) cc_final: 0.7919 (t) REVERT: G 88 TYR cc_start: 0.7817 (m-80) cc_final: 0.7580 (m-80) REVERT: B 391 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8315 (mp) REVERT: B 509 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.6419 (pp30) REVERT: B 511 ARG cc_start: 0.7774 (mmp-170) cc_final: 0.7057 (tpp80) REVERT: B 538 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6830 (mttm) REVERT: B 539 ASN cc_start: 0.7977 (m-40) cc_final: 0.7551 (m-40) REVERT: C 128 MET cc_start: 0.7957 (tpp) cc_final: 0.7692 (tpp) REVERT: C 147 GLN cc_start: 0.7793 (mt0) cc_final: 0.7450 (mt0) REVERT: C 244 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7363 (p0) REVERT: C 388 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7568 (mtp180) REVERT: C 479 GLN cc_start: 0.7804 (mp10) cc_final: 0.7417 (mm110) REVERT: C 483 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: C 511 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7351 (tpp80) REVERT: C 541 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7583 (t) outliers start: 68 outliers final: 35 residues processed: 247 average time/residue: 1.2625 time to fit residues: 348.3283 Evaluate side-chains 214 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 F residue 73 SER Chi-restraints excluded: chain F residue 118 VAL 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 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 B residue 622 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 244 ASN Chi-restraints excluded: chain C residue 305 ASP 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 180 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16182 Z= 0.316 Angle : 0.592 10.555 22032 Z= 0.304 Chirality : 0.047 0.152 2376 Planarity : 0.005 0.044 2859 Dihedral : 4.642 19.181 2175 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.53 % Allowed : 11.79 % Favored : 83.68 % 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: 0.14 (0.19), residues: 1980 helix: -0.32 (0.60), residues: 81 sheet: 0.45 (0.17), residues: 867 loop : -0.09 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 47 HIS 0.007 0.001 HIS A 114 PHE 0.013 0.002 PHE G 24 TYR 0.017 0.002 TYR C 203 ARG 0.004 0.000 ARG F 74 *********************** 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 253 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 175 time to evaluate : 2.370 Fit side-chains REVERT: A 128 MET cc_start: 0.8012 (tpp) cc_final: 0.7779 (tpt) REVERT: A 133 GLN cc_start: 0.7392 (mm110) cc_final: 0.7011 (mm-40) REVERT: A 147 GLN cc_start: 0.7666 (mt0) cc_final: 0.7327 (mt0) REVERT: A 151 GLU cc_start: 0.7679 (tp30) cc_final: 0.7366 (mm-30) REVERT: A 305 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5841 (m-30) REVERT: A 478 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7690 (p0) REVERT: A 479 GLN cc_start: 0.8021 (mp10) cc_final: 0.7525 (mm110) REVERT: A 509 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.6613 (pp30) REVERT: A 538 LYS cc_start: 0.7478 (mtpt) cc_final: 0.7132 (mtmm) REVERT: A 539 ASN cc_start: 0.8033 (m110) cc_final: 0.7570 (m-40) REVERT: A 611 ASP cc_start: 0.7646 (m-30) cc_final: 0.7304 (m-30) REVERT: D 46 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: E 59 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7694 (t) REVERT: G 5 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7251 (mp) REVERT: B 221 MET cc_start: 0.7666 (mmm) cc_final: 0.7463 (mmm) REVERT: B 350 ILE cc_start: 0.1808 (OUTLIER) cc_final: 0.1424 (pp) REVERT: B 391 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8307 (mt) REVERT: B 497 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8942 (mm) REVERT: B 498 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7102 (mmm) REVERT: B 509 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.6364 (pp30) REVERT: B 512 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.7982 (p0) REVERT: B 538 LYS cc_start: 0.7457 (mtpt) cc_final: 0.6893 (mttm) REVERT: B 539 ASN cc_start: 0.7980 (m-40) cc_final: 0.7573 (m-40) REVERT: C 202 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7040 (mt-10) REVERT: C 391 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8585 (mp) REVERT: C 479 GLN cc_start: 0.7880 (mp10) cc_final: 0.7428 (mm110) REVERT: C 483 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: C 511 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7340 (tpp80) outliers start: 78 outliers final: 45 residues processed: 232 average time/residue: 1.3246 time to fit residues: 342.1654 Evaluate side-chains 227 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 405 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 478 ASP 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 18 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 E residue 85 MET Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 5 ILE 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 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 497 ILE 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 166 VAL 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 379 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 612 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 144 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN C 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16182 Z= 0.374 Angle : 0.625 10.735 22032 Z= 0.322 Chirality : 0.048 0.159 2376 Planarity : 0.005 0.043 2859 Dihedral : 4.858 20.198 2175 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.99 % Allowed : 13.18 % Favored : 81.82 % 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: 0.06 (0.19), residues: 1980 helix: -0.46 (0.59), residues: 81 sheet: 0.37 (0.17), residues: 918 loop : -0.12 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 474 HIS 0.009 0.002 HIS B 246 PHE 0.017 0.002 PHE G 24 TYR 0.015 0.002 TYR A 561 ARG 0.005 0.001 ARG C 308 *********************** 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 264 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 178 time to evaluate : 1.698 Fit side-chains REVERT: A 133 GLN cc_start: 0.7352 (mm110) cc_final: 0.6994 (mm-40) REVERT: A 147 GLN cc_start: 0.7707 (mt0) cc_final: 0.7355 (mt0) REVERT: A 151 GLU cc_start: 0.7696 (tp30) cc_final: 0.7487 (tp30) REVERT: A 244 ASN cc_start: 0.7551 (p0) cc_final: 0.7348 (p0) REVERT: A 305 ASP cc_start: 0.6240 (OUTLIER) cc_final: 0.5850 (m-30) REVERT: A 479 GLN cc_start: 0.7984 (mp10) cc_final: 0.7453 (mm110) REVERT: A 509 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.6684 (pp30) REVERT: A 538 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7190 (mtmm) REVERT: A 611 ASP cc_start: 0.7645 (m-30) cc_final: 0.7398 (m-30) REVERT: D 46 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: E 59 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7737 (t) REVERT: F 118 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7862 (p) REVERT: G 21 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7767 (t) REVERT: G 88 TYR cc_start: 0.7887 (m-80) cc_final: 0.7642 (m-80) REVERT: B 163 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: B 350 ILE cc_start: 0.1968 (OUTLIER) cc_final: 0.1566 (pp) REVERT: B 391 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 498 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7154 (mmm) REVERT: B 509 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.6481 (pp30) REVERT: B 511 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6799 (mmp-170) REVERT: B 512 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8054 (p0) REVERT: B 538 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7083 (mttm) REVERT: C 147 GLN cc_start: 0.7920 (mt0) cc_final: 0.7640 (mt0) REVERT: C 202 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7150 (mt-10) REVERT: C 305 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5908 (t0) REVERT: C 391 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8572 (mp) REVERT: C 477 SER cc_start: 0.8536 (t) cc_final: 0.8243 (m) REVERT: C 479 GLN cc_start: 0.7883 (mp10) cc_final: 0.7573 (mm110) REVERT: C 483 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: C 511 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7317 (tpp80) REVERT: C 512 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8082 (p0) outliers start: 86 outliers final: 48 residues processed: 237 average time/residue: 1.2973 time to fit residues: 342.2670 Evaluate side-chains 234 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 169 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 103 MET 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 E residue 106 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 118 VAL 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 90 LEU 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 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 511 ARG 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 305 ASP Chi-restraints excluded: chain C residue 379 SER 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 512 ASP 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 65 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16182 Z= 0.257 Angle : 0.555 9.683 22032 Z= 0.284 Chirality : 0.046 0.145 2376 Planarity : 0.005 0.042 2859 Dihedral : 4.630 19.406 2175 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.18 % Allowed : 14.75 % Favored : 81.07 % 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: 0.13 (0.19), residues: 1980 helix: -0.32 (0.59), residues: 81 sheet: 0.42 (0.17), residues: 870 loop : -0.07 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.005 0.001 HIS A 114 PHE 0.010 0.001 PHE I 24 TYR 0.015 0.001 TYR C 203 ARG 0.004 0.000 ARG E 74 *********************** 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 245 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 173 time to evaluate : 1.927 Fit side-chains REVERT: A 133 GLN cc_start: 0.7265 (mm110) cc_final: 0.6996 (mm-40) REVERT: A 147 GLN cc_start: 0.7605 (mt0) cc_final: 0.7294 (mt0) REVERT: A 151 GLU cc_start: 0.7671 (tp30) cc_final: 0.7407 (tp30) REVERT: A 305 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5851 (m-30) REVERT: A 479 GLN cc_start: 0.7920 (mp10) cc_final: 0.7423 (mm110) REVERT: A 509 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.6564 (pp30) REVERT: A 538 LYS cc_start: 0.7485 (mtpt) cc_final: 0.7187 (mtmm) REVERT: A 611 ASP cc_start: 0.7578 (m-30) cc_final: 0.7310 (m-30) REVERT: D 46 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: E 59 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7727 (t) REVERT: G 21 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7852 (t) REVERT: G 88 TYR cc_start: 0.7877 (m-80) cc_final: 0.7643 (m-80) REVERT: I 105 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6846 (t) REVERT: B 350 ILE cc_start: 0.2116 (OUTLIER) cc_final: 0.1748 (pp) REVERT: B 391 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8276 (mt) REVERT: B 498 MET cc_start: 0.7529 (mmm) cc_final: 0.7101 (mmm) REVERT: B 512 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8288 (p0) REVERT: B 538 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7082 (mttm) REVERT: C 147 GLN cc_start: 0.7888 (mt0) cc_final: 0.7619 (mt0) REVERT: C 202 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7125 (mt-10) REVERT: C 305 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5960 (t0) REVERT: C 391 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8517 (mp) REVERT: C 477 SER cc_start: 0.8506 (t) cc_final: 0.8239 (m) REVERT: C 479 GLN cc_start: 0.7886 (mp10) cc_final: 0.7519 (mm110) REVERT: C 483 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: C 511 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7300 (tpp80) outliers start: 72 outliers final: 42 residues processed: 225 average time/residue: 1.3168 time to fit residues: 332.7322 Evaluate side-chains 221 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 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 48 LEU 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 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 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 483 GLN Chi-restraints excluded: chain B residue 505 GLU 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 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 379 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 193 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16182 Z= 0.243 Angle : 0.551 9.469 22032 Z= 0.282 Chirality : 0.046 0.143 2376 Planarity : 0.005 0.042 2859 Dihedral : 4.545 19.163 2175 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.89 % Allowed : 15.27 % Favored : 80.84 % 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: -0.20 (0.60), residues: 81 sheet: 0.47 (0.17), residues: 891 loop : -0.02 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 474 HIS 0.005 0.001 HIS A 114 PHE 0.009 0.001 PHE I 24 TYR 0.015 0.001 TYR C 203 ARG 0.003 0.000 ARG E 74 *********************** 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 236 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 169 time to evaluate : 1.925 Fit side-chains REVERT: A 133 GLN cc_start: 0.7268 (mm110) cc_final: 0.6996 (mm-40) REVERT: A 147 GLN cc_start: 0.7607 (mt0) cc_final: 0.7285 (mt0) REVERT: A 151 GLU cc_start: 0.7700 (tp30) cc_final: 0.7460 (tp30) REVERT: A 479 GLN cc_start: 0.7943 (mp10) cc_final: 0.7443 (mm110) REVERT: A 509 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.6588 (pp30) REVERT: A 538 LYS cc_start: 0.7487 (mtpt) cc_final: 0.7201 (mtmm) REVERT: A 611 ASP cc_start: 0.7559 (m-30) cc_final: 0.7314 (m-30) REVERT: D 46 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: E 46 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: E 59 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7737 (t) REVERT: G 21 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7851 (t) REVERT: I 105 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6973 (t) REVERT: B 163 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: B 189 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6899 (tp30) REVERT: B 350 ILE cc_start: 0.2015 (OUTLIER) cc_final: 0.1680 (pp) REVERT: B 498 MET cc_start: 0.7514 (mmm) cc_final: 0.7167 (mmm) REVERT: B 512 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8316 (p0) REVERT: B 538 LYS cc_start: 0.7512 (mtpt) cc_final: 0.7084 (mttm) REVERT: C 76 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8256 (mttt) REVERT: C 147 GLN cc_start: 0.7853 (mt0) cc_final: 0.7597 (mt0) REVERT: C 202 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7171 (mt-10) REVERT: C 305 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5798 (t0) REVERT: C 391 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 477 SER cc_start: 0.8495 (t) cc_final: 0.8248 (m) REVERT: C 479 GLN cc_start: 0.7915 (mp10) cc_final: 0.7541 (mm110) REVERT: C 511 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7315 (tpp80) outliers start: 67 outliers final: 45 residues processed: 219 average time/residue: 1.3128 time to fit residues: 321.9605 Evaluate side-chains 223 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 165 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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 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 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 46 GLU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 118 VAL 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 90 LEU 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 189 GLU 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 473 THR Chi-restraints excluded: chain B residue 483 GLN 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 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 379 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** C 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16182 Z= 0.189 Angle : 0.521 8.909 22032 Z= 0.266 Chirality : 0.045 0.143 2376 Planarity : 0.004 0.042 2859 Dihedral : 4.376 18.889 2175 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.54 % Allowed : 16.43 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.19), residues: 1980 helix: -0.10 (0.60), residues: 81 sheet: 0.53 (0.18), residues: 858 loop : 0.09 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 474 HIS 0.004 0.001 HIS A 114 PHE 0.007 0.001 PHE H 24 TYR 0.016 0.001 TYR C 203 ARG 0.003 0.000 ARG E 74 *********************** 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 236 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 175 time to evaluate : 1.995 Fit side-chains REVERT: A 75 ASN cc_start: 0.7967 (p0) cc_final: 0.7218 (p0) REVERT: A 133 GLN cc_start: 0.7201 (mm110) cc_final: 0.6949 (mm-40) REVERT: A 147 GLN cc_start: 0.7461 (mt0) cc_final: 0.7162 (mt0) REVERT: A 151 GLU cc_start: 0.7651 (tp30) cc_final: 0.7426 (tp30) REVERT: A 174 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (mtp180) REVERT: A 479 GLN cc_start: 0.7911 (mp10) cc_final: 0.7420 (mm110) REVERT: A 509 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6544 (pp30) REVERT: A 538 LYS cc_start: 0.7500 (mtpt) cc_final: 0.7224 (mtmm) REVERT: A 611 ASP cc_start: 0.7551 (m-30) cc_final: 0.7321 (m-30) REVERT: D 46 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: E 59 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7714 (t) REVERT: G 21 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7860 (t) REVERT: B 350 ILE cc_start: 0.1994 (OUTLIER) cc_final: 0.1665 (pp) REVERT: B 391 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8245 (mt) REVERT: B 498 MET cc_start: 0.7372 (mmm) cc_final: 0.7059 (mmm) REVERT: B 538 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7072 (mttm) REVERT: C 147 GLN cc_start: 0.7805 (mt0) cc_final: 0.7560 (mt0) REVERT: C 305 ASP cc_start: 0.6345 (OUTLIER) cc_final: 0.5971 (t0) REVERT: C 477 SER cc_start: 0.8497 (t) cc_final: 0.8227 (m) REVERT: C 479 GLN cc_start: 0.7897 (mp10) cc_final: 0.7529 (mm110) REVERT: C 511 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7335 (tpp80) outliers start: 61 outliers final: 38 residues processed: 222 average time/residue: 1.3446 time to fit residues: 333.3029 Evaluate side-chains 208 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 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 7 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 I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain B residue 90 LEU 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 580 MET Chi-restraints excluded: chain B residue 606 PHE 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 305 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 541 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** H 33 ASN B 246 HIS B 483 GLN C 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16182 Z= 0.189 Angle : 0.522 8.821 22032 Z= 0.266 Chirality : 0.045 0.140 2376 Planarity : 0.004 0.042 2859 Dihedral : 4.300 18.507 2175 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.25 % Allowed : 16.90 % Favored : 79.85 % 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: 0.42 (0.19), residues: 1980 helix: -0.04 (0.60), residues: 81 sheet: 0.59 (0.18), residues: 840 loop : 0.16 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 336 HIS 0.004 0.001 HIS A 114 PHE 0.007 0.001 PHE G 24 TYR 0.019 0.001 TYR C 203 ARG 0.003 0.000 ARG C 192 *********************** 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 223 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 1.764 Fit side-chains REVERT: A 75 ASN cc_start: 0.7950 (p0) cc_final: 0.7150 (p0) REVERT: A 133 GLN cc_start: 0.7255 (mm110) cc_final: 0.6942 (mm-40) REVERT: A 147 GLN cc_start: 0.7461 (mt0) cc_final: 0.7165 (mt0) REVERT: A 151 GLU cc_start: 0.7649 (tp30) cc_final: 0.7410 (tp30) REVERT: A 174 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7466 (mtp180) REVERT: A 219 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.6621 (t0) REVERT: A 479 GLN cc_start: 0.7883 (mp10) cc_final: 0.7384 (mm110) REVERT: A 498 MET cc_start: 0.7598 (mmm) cc_final: 0.7102 (mmm) REVERT: A 509 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6552 (pp30) REVERT: A 538 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7239 (mtmm) REVERT: A 611 ASP cc_start: 0.7571 (m-30) cc_final: 0.7335 (m-30) REVERT: D 46 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: E 59 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7730 (t) REVERT: G 21 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7868 (t) REVERT: B 244 ASN cc_start: 0.7565 (p0) cc_final: 0.7195 (p0) REVERT: B 350 ILE cc_start: 0.2072 (OUTLIER) cc_final: 0.1765 (pp) REVERT: B 391 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 498 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7035 (mmm) REVERT: B 538 LYS cc_start: 0.7516 (mtpt) cc_final: 0.7091 (mttm) REVERT: C 76 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8217 (mttt) REVERT: C 147 GLN cc_start: 0.7833 (mt0) cc_final: 0.7471 (mp10) REVERT: C 305 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.5972 (t0) REVERT: C 391 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 477 SER cc_start: 0.8491 (t) cc_final: 0.8213 (m) REVERT: C 479 GLN cc_start: 0.7901 (mp10) cc_final: 0.7528 (mm110) REVERT: C 511 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7341 (tpp80) outliers start: 56 outliers final: 42 residues processed: 213 average time/residue: 1.3312 time to fit residues: 316.6434 Evaluate side-chains 218 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 164 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 219 ASP 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 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 106 LEU 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 B residue 90 LEU 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 498 MET Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 606 PHE 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 305 ASP Chi-restraints excluded: chain C residue 379 SER 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 190 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN B 246 HIS B 483 GLN C 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16182 Z= 0.312 Angle : 0.583 9.521 22032 Z= 0.299 Chirality : 0.047 0.147 2376 Planarity : 0.005 0.041 2859 Dihedral : 4.573 19.893 2175 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.72 % Allowed : 16.96 % Favored : 79.33 % 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: 0.32 (0.19), residues: 1980 helix: -0.24 (0.59), residues: 81 sheet: 0.55 (0.17), residues: 873 loop : 0.06 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 474 HIS 0.005 0.001 HIS A 114 PHE 0.011 0.002 PHE G 24 TYR 0.015 0.002 TYR A 561 ARG 0.003 0.000 ARG B 307 ********************** 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 229 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 165 time to evaluate : 1.734 Fit side-chains REVERT: A 75 ASN cc_start: 0.8013 (p0) cc_final: 0.7200 (p0) REVERT: A 133 GLN cc_start: 0.7311 (mm110) cc_final: 0.6994 (mm-40) REVERT: A 147 GLN cc_start: 0.7625 (mt0) cc_final: 0.7303 (mt0) REVERT: A 174 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: A 479 GLN cc_start: 0.7956 (mp10) cc_final: 0.7430 (mm110) REVERT: A 509 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.6630 (pp30) REVERT: A 538 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7229 (mtmm) REVERT: A 611 ASP cc_start: 0.7586 (m-30) cc_final: 0.7324 (m-30) REVERT: D 38 ARG cc_start: 0.7908 (ptt180) cc_final: 0.7654 (ptt180) REVERT: D 46 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: E 59 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7790 (t) REVERT: G 21 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7871 (t) REVERT: B 189 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: B 350 ILE cc_start: 0.1822 (OUTLIER) cc_final: 0.1439 (pp) REVERT: B 391 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8318 (mt) REVERT: B 498 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7139 (mmm) REVERT: B 538 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7108 (mttm) REVERT: C 147 GLN cc_start: 0.7888 (mt0) cc_final: 0.7518 (mp10) REVERT: C 305 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.6099 (t0) REVERT: C 391 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8547 (mp) REVERT: C 477 SER cc_start: 0.8477 (t) cc_final: 0.8202 (m) REVERT: C 479 GLN cc_start: 0.7933 (mp10) cc_final: 0.7568 (mm110) REVERT: C 511 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7321 (tpp80) outliers start: 64 outliers final: 45 residues processed: 217 average time/residue: 1.3225 time to fit residues: 320.8333 Evaluate side-chains 220 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 164 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain 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 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 B residue 90 LEU Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 189 GLU 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 505 GLU Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 606 PHE 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 305 ASP Chi-restraints excluded: chain C residue 379 SER 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 169 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 66 optimal weight: 0.0170 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- 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** 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 = 0.4033 r_free = 0.4033 target = 0.180782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126358 restraints weight = 17641.436| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.43 r_work: 0.3146 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16182 Z= 0.287 Angle : 0.567 9.318 22032 Z= 0.290 Chirality : 0.046 0.145 2376 Planarity : 0.005 0.040 2859 Dihedral : 4.548 19.781 2175 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.54 % Allowed : 17.31 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.19), residues: 1980 helix: -0.22 (0.60), residues: 81 sheet: 0.56 (0.17), residues: 873 loop : 0.06 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.005 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.04 seconds wall clock time: 107 minutes 46.75 seconds (6466.75 seconds total)