Starting phenix.real_space_refine on Sun May 18 13:18:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3o_38893/05_2025/8y3o_38893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3o_38893/05_2025/8y3o_38893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3o_38893/05_2025/8y3o_38893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3o_38893/05_2025/8y3o_38893.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3o_38893/05_2025/8y3o_38893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3o_38893/05_2025/8y3o_38893.cif" } resolution = 2.75 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= 0.001 sd= 0.128 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 10884 2.51 5 N 2925 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17058 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "D" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 906 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "G" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 906 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "F" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 906 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 9.51, per 1000 atoms: 0.56 Number of scatterers: 17058 At special positions: 0 Unit cell: (130, 122.72, 130, 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 3177 8.00 N 2925 7.00 C 10884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 109 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 109 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 98 " distance=2.03 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 109 " distance=2.04 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: 3.85 Conformation dependent library (CDL) restraints added in 2.1 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 43 sheets defined 9.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'C' and resid 129 through 133 removed outlier: 4.047A pdb=" N GLY C 132 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.567A pdb=" N LEU C 343 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 344' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 555 through 566 Proline residue: C 563 - end of helix Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.030A pdb=" N THR H 93 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.169A pdb=" N GLY A 132 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.532A pdb=" N LEU A 343 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 344' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 555 through 566 Proline residue: A 563 - end of helix Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 89 through 93 removed outlier: 4.031A pdb=" N THR G 93 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.097A pdb=" N GLY B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.555A pdb=" N LEU B 343 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 344' Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 555 through 566 Proline residue: B 563 - end of helix Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 89 through 93 removed outlier: 4.019A pdb=" N THR I 93 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 72 through 75 removed outlier: 5.489A pdb=" N ASN C 409 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE C 109 " --> pdb=" O ASN C 409 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 89 through 93 removed outlier: 4.112A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AA5, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.143A pdb=" N SER C 387 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER C 521 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER C 523 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 391 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 234 through 246 removed outlier: 5.363A pdb=" N ASN C 309 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 307 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 242 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP C 305 " --> pdb=" O LEU C 242 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 305 through 314 current: chain 'C' and resid 528 through 534 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 528 through 534 current: chain 'A' and resid 305 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 305 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 305 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 305 through 314 current: chain 'B' and resid 528 through 534 Processing sheet with id=AA8, first strand: chain 'C' and resid 436 through 439 Processing sheet with id=AA9, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'D' and resid 57 through 58 removed outlier: 6.501A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR D 53 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.745A pdb=" N VAL H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 72 through 75 removed outlier: 5.469A pdb=" N ASN A 409 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 109 " --> pdb=" O ASN A 409 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 89 through 93 removed outlier: 4.035A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AC1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AC2, first strand: chain 'A' and resid 153 through 158 removed outlier: 6.172A pdb=" N SER A 387 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER A 521 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 523 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 391 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AC4, first strand: chain 'A' and resid 436 through 439 Processing sheet with id=AC5, first strand: chain 'A' and resid 444 through 446 Processing sheet with id=AC6, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AC7, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AC9, first strand: chain 'E' and resid 57 through 58 removed outlier: 5.362A pdb=" N LEU E 50 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN E 41 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.765A pdb=" N VAL G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 72 through 75 removed outlier: 5.461A pdb=" N ASN B 409 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 109 " --> pdb=" O ASN B 409 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 89 through 93 removed outlier: 4.062A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AD6, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AD7, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.131A pdb=" N SER B 387 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER B 521 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER B 523 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 391 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 176 through 179 Processing sheet with id=AD9, first strand: chain 'B' and resid 436 through 439 Processing sheet with id=AE1, first strand: chain 'B' and resid 444 through 446 Processing sheet with id=AE2, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AE3, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'F' and resid 57 through 58 removed outlier: 5.340A pdb=" N LEU F 50 " --> pdb=" O GLN F 41 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN F 41 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.755A pdb=" N VAL I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY I 50 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1236 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: 5.38 Time building geometry restraints manager: 4.52 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: 5503 1.34 - 1.46: 4164 1.46 - 1.58: 7766 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 17538 Sorted by residual: bond pdb=" C THR F 7 " pdb=" N PRO F 8 " ideal model delta sigma weight residual 1.334 1.368 -0.034 1.11e-02 8.12e+03 9.65e+00 bond pdb=" C THR E 7 " pdb=" N PRO E 8 " ideal model delta sigma weight residual 1.331 1.367 -0.035 1.28e-02 6.10e+03 7.65e+00 bond pdb=" CA GLY E 72 " pdb=" C GLY E 72 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.68e+00 bond pdb=" CB ASP A 611 " pdb=" CG ASP A 611 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.47e+00 bond pdb=" N GLY E 72 " pdb=" CA GLY E 72 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.03e+00 ... (remaining 17533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 23127 1.97 - 3.94: 619 3.94 - 5.91: 82 5.91 - 7.88: 13 7.88 - 9.85: 9 Bond angle restraints: 23850 Sorted by residual: angle pdb=" CA MET B 466 " pdb=" CB MET B 466 " pdb=" CG MET B 466 " ideal model delta sigma weight residual 114.10 122.45 -8.35 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CA PRO A 84 " pdb=" N PRO A 84 " pdb=" CD PRO A 84 " ideal model delta sigma weight residual 112.00 106.62 5.38 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CB MET H 103 " pdb=" CG MET H 103 " pdb=" SD MET H 103 " ideal model delta sigma weight residual 112.70 122.55 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CB MET G 103 " pdb=" CG MET G 103 " pdb=" SD MET G 103 " ideal model delta sigma weight residual 112.70 122.45 -9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C ASP B 551 " pdb=" N LYS B 552 " pdb=" CA LYS B 552 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 23845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 9366 17.49 - 34.97: 823 34.97 - 52.46: 99 52.46 - 69.94: 16 69.94 - 87.43: 19 Dihedral angle restraints: 10323 sinusoidal: 4128 harmonic: 6195 Sorted by residual: dihedral pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " pdb=" SG CYS H 109 " pdb=" CB CYS H 109 " ideal model delta sinusoidal sigma weight residual 93.00 48.50 44.50 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS G 101 " pdb=" SG CYS G 101 " pdb=" SG CYS G 109 " pdb=" CB CYS G 109 " ideal model delta sinusoidal sigma weight residual 93.00 49.82 43.18 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS I 101 " pdb=" SG CYS I 101 " pdb=" SG CYS I 109 " pdb=" CB CYS I 109 " ideal model delta sinusoidal sigma weight residual 93.00 49.88 43.12 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 10320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1954 0.056 - 0.111: 482 0.111 - 0.167: 100 0.167 - 0.223: 7 0.223 - 0.279: 4 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB THR E 76 " pdb=" CA THR E 76 " pdb=" OG1 THR E 76 " pdb=" CG2 THR E 76 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB THR F 76 " pdb=" CA THR F 76 " pdb=" OG1 THR F 76 " pdb=" CG2 THR F 76 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB THR D 76 " pdb=" CA THR D 76 " pdb=" OG1 THR D 76 " pdb=" CG2 THR D 76 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2544 not shown) Planarity restraints: 3099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 83 " 0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO A 84 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 83 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 84 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 159 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO B 160 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.034 5.00e-02 4.00e+02 ... (remaining 3096 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1661 2.75 - 3.29: 15201 3.29 - 3.83: 28500 3.83 - 4.36: 34372 4.36 - 4.90: 60530 Nonbonded interactions: 140264 Sorted by model distance: nonbonded pdb=" O ALA F 55 " pdb=" OG SER F 69 " model vdw 2.217 3.040 nonbonded pdb=" O ALA D 55 " pdb=" OG SER D 69 " model vdw 2.225 3.040 nonbonded pdb=" O ALA E 55 " pdb=" OG SER E 69 " model vdw 2.230 3.040 nonbonded pdb=" OG SER I 17 " pdb=" OE1 GLN I 84 " model vdw 2.234 3.040 nonbonded pdb=" O THR C 446 " pdb=" OG1 THR C 620 " model vdw 2.250 3.040 ... (remaining 140259 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: 0.04 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.900 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 0.039 17547 Z= 0.168 Angle : 0.745 9.845 23868 Z= 0.394 Chirality : 0.051 0.279 2547 Planarity : 0.007 0.122 3099 Dihedral : 13.070 87.429 6342 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2127 helix: -2.30 (0.42), residues: 111 sheet: -0.45 (0.17), residues: 915 loop : -0.96 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 61 HIS 0.013 0.001 HIS B 80 PHE 0.019 0.001 PHE B 467 TYR 0.021 0.002 TYR G 62 ARG 0.009 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.11561 ( 493) hydrogen bonds : angle 7.09858 ( 1236) SS BOND : bond 0.00564 ( 9) SS BOND : angle 0.87284 ( 18) covalent geometry : bond 0.00346 (17538) covalent geometry : angle 0.74501 (23850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.753 Fit side-chains REVERT: A 221 MET cc_start: 0.6921 (tpt) cc_final: 0.6691 (tpt) REVERT: B 148 THR cc_start: 0.7976 (p) cc_final: 0.7768 (p) REVERT: B 538 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6276 (mppt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 1.2095 time to fit residues: 340.9208 Evaluate side-chains 209 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 475 ASN C 502 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN B 80 HIS B 230 GLN B 475 ASN B 502 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.170609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125643 restraints weight = 22811.236| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.62 r_work: 0.3444 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17547 Z= 0.258 Angle : 0.659 9.458 23868 Z= 0.341 Chirality : 0.049 0.162 2547 Planarity : 0.006 0.077 3099 Dihedral : 5.147 18.750 2337 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.49 % Allowed : 10.03 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2127 helix: -2.78 (0.42), residues: 99 sheet: -0.46 (0.17), residues: 903 loop : -0.81 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 61 HIS 0.017 0.002 HIS C 80 PHE 0.015 0.002 PHE B 137 TYR 0.013 0.002 TYR G 96 ARG 0.008 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 493) hydrogen bonds : angle 6.56129 ( 1236) SS BOND : bond 0.00447 ( 9) SS BOND : angle 1.30592 ( 18) covalent geometry : bond 0.00603 (17538) covalent geometry : angle 0.65794 (23850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 1.935 Fit side-chains REVERT: C 221 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6034 (tpp) REVERT: C 479 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7883 (mt0) REVERT: C 486 ASP cc_start: 0.8427 (m-30) cc_final: 0.8223 (m-30) REVERT: D 109 GLU cc_start: 0.5578 (tp30) cc_final: 0.5043 (tp30) REVERT: H 100 GLU cc_start: 0.8348 (tt0) cc_final: 0.7958 (tt0) REVERT: A 230 GLN cc_start: 0.7971 (tp40) cc_final: 0.7664 (tp-100) REVERT: E 111 LYS cc_start: 0.5707 (OUTLIER) cc_final: 0.4998 (tptm) REVERT: G 19 LYS cc_start: 0.8541 (tptt) cc_final: 0.8325 (tptm) REVERT: G 38 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7147 (ptt180) REVERT: B 244 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8087 (p0) REVERT: B 409 ASN cc_start: 0.8320 (m110) cc_final: 0.8018 (m110) REVERT: B 466 MET cc_start: 0.6870 (tpt) cc_final: 0.6580 (mmm) REVERT: F 27 GLN cc_start: 0.7992 (pm20) cc_final: 0.7442 (pm20) REVERT: F 111 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5373 (tppt) outliers start: 28 outliers final: 14 residues processed: 243 average time/residue: 1.2006 time to fit residues: 330.1349 Evaluate side-chains 229 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 190 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 502 HIS A 80 HIS A 483 GLN A 502 HIS G 86 ASN B 80 HIS B 230 GLN B 483 GLN B 502 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127319 restraints weight = 22627.501| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.63 r_work: 0.3471 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17547 Z= 0.168 Angle : 0.569 8.333 23868 Z= 0.293 Chirality : 0.046 0.158 2547 Planarity : 0.005 0.060 3099 Dihedral : 4.780 17.321 2337 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.19 % Allowed : 13.07 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2127 helix: -2.51 (0.44), residues: 99 sheet: -0.48 (0.17), residues: 903 loop : -0.74 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 336 HIS 0.014 0.001 HIS A 80 PHE 0.010 0.001 PHE F 93 TYR 0.010 0.001 TYR B 203 ARG 0.007 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 493) hydrogen bonds : angle 6.32300 ( 1236) SS BOND : bond 0.00438 ( 9) SS BOND : angle 1.13046 ( 18) covalent geometry : bond 0.00388 (17538) covalent geometry : angle 0.56840 (23850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 1.760 Fit side-chains REVERT: C 133 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: C 221 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6258 (tpp) REVERT: C 305 ASP cc_start: 0.7584 (t0) cc_final: 0.7197 (t0) REVERT: C 479 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7935 (mt0) REVERT: C 498 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.5853 (mpt) REVERT: D 109 GLU cc_start: 0.5447 (tp30) cc_final: 0.4998 (tp30) REVERT: H 46 GLU cc_start: 0.7904 (tt0) cc_final: 0.7317 (mt-10) REVERT: A 133 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6726 (tt0) REVERT: A 203 TYR cc_start: 0.7269 (p90) cc_final: 0.6905 (p90) REVERT: A 230 GLN cc_start: 0.8097 (tp40) cc_final: 0.7792 (tp-100) REVERT: A 498 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.5934 (mpt) REVERT: E 27 GLN cc_start: 0.8210 (pm20) cc_final: 0.7432 (pm20) REVERT: G 38 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7027 (ptt180) REVERT: B 466 MET cc_start: 0.6948 (tpt) cc_final: 0.6655 (mmm) REVERT: B 580 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7230 (mpp) REVERT: F 27 GLN cc_start: 0.7962 (pm20) cc_final: 0.7205 (pm20) REVERT: F 111 LYS cc_start: 0.5653 (OUTLIER) cc_final: 0.5433 (tppt) outliers start: 41 outliers final: 13 residues processed: 251 average time/residue: 1.1781 time to fit residues: 332.7419 Evaluate side-chains 241 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 101 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 488 HIS C 502 HIS H 86 ASN A 80 HIS A 502 HIS G 86 ASN B 80 HIS B 502 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123085 restraints weight = 22770.219| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.56 r_work: 0.3414 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 17547 Z= 0.326 Angle : 0.700 9.643 23868 Z= 0.362 Chirality : 0.050 0.167 2547 Planarity : 0.006 0.056 3099 Dihedral : 5.389 22.196 2337 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.47 % Allowed : 15.36 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2127 helix: -2.77 (0.35), residues: 135 sheet: -0.79 (0.16), residues: 963 loop : -0.76 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 336 HIS 0.016 0.002 HIS A 80 PHE 0.015 0.002 PHE F 93 TYR 0.024 0.002 TYR H 96 ARG 0.008 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 493) hydrogen bonds : angle 6.85920 ( 1236) SS BOND : bond 0.00477 ( 9) SS BOND : angle 1.39179 ( 18) covalent geometry : bond 0.00768 (17538) covalent geometry : angle 0.69874 (23850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 1.829 Fit side-chains REVERT: C 133 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: C 305 ASP cc_start: 0.7634 (t0) cc_final: 0.7061 (t0) REVERT: C 391 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 479 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7988 (mt0) REVERT: C 498 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.6056 (mpt) REVERT: C 613 ASP cc_start: 0.7592 (m-30) cc_final: 0.6999 (t0) REVERT: D 91 TYR cc_start: 0.8236 (m-80) cc_final: 0.7898 (m-80) REVERT: H 76 ASN cc_start: 0.8636 (m-40) cc_final: 0.8323 (m110) REVERT: A 133 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: A 230 GLN cc_start: 0.8177 (tp40) cc_final: 0.7844 (tp-100) REVERT: A 580 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7299 (mmt) REVERT: E 111 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5132 (tptm) REVERT: G 38 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7109 (ptt180) REVERT: B 104 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6564 (ptt) REVERT: B 230 GLN cc_start: 0.8267 (tp40) cc_final: 0.7928 (tp-100) REVERT: B 244 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8253 (p0) REVERT: B 466 MET cc_start: 0.7035 (tpt) cc_final: 0.6646 (mmm) REVERT: B 580 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: F 27 GLN cc_start: 0.8088 (pm20) cc_final: 0.7556 (pm20) REVERT: F 64 GLU cc_start: 0.7769 (tp30) cc_final: 0.6679 (mp0) outliers start: 65 outliers final: 22 residues processed: 262 average time/residue: 1.1106 time to fit residues: 329.3888 Evaluate side-chains 245 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 146 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 196 optimal weight: 0.0170 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 502 HIS H 86 ASN A 80 HIS G 86 ASN B 80 HIS B 502 HIS F 35 ASN I 86 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.174937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130672 restraints weight = 22982.427| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.66 r_work: 0.3492 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17547 Z= 0.110 Angle : 0.534 7.297 23868 Z= 0.273 Chirality : 0.045 0.158 2547 Planarity : 0.004 0.048 3099 Dihedral : 4.572 17.581 2337 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.77 % Allowed : 16.48 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2127 helix: -2.27 (0.47), residues: 99 sheet: -0.62 (0.17), residues: 909 loop : -0.69 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 336 HIS 0.015 0.001 HIS A 80 PHE 0.009 0.001 PHE A 337 TYR 0.011 0.001 TYR C 203 ARG 0.010 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 493) hydrogen bonds : angle 6.13693 ( 1236) SS BOND : bond 0.00462 ( 9) SS BOND : angle 1.01414 ( 18) covalent geometry : bond 0.00248 (17538) covalent geometry : angle 0.53360 (23850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.952 Fit side-chains REVERT: D 91 TYR cc_start: 0.8131 (m-80) cc_final: 0.7786 (m-80) REVERT: H 46 GLU cc_start: 0.7828 (tt0) cc_final: 0.7120 (mt-10) REVERT: A 133 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: A 203 TYR cc_start: 0.7083 (p90) cc_final: 0.6850 (p90) REVERT: A 230 GLN cc_start: 0.8064 (tp40) cc_final: 0.7789 (tp-100) REVERT: A 456 MET cc_start: 0.0843 (ppp) cc_final: -0.1010 (ppp) REVERT: G 38 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7958 (ptm160) REVERT: G 84 GLN cc_start: 0.7938 (tp40) cc_final: 0.7626 (tp40) REVERT: B 133 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6604 (tt0) REVERT: B 230 GLN cc_start: 0.8200 (tp40) cc_final: 0.7850 (tp-100) REVERT: B 244 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8068 (p0) REVERT: B 466 MET cc_start: 0.7060 (tpt) cc_final: 0.6754 (mmm) REVERT: B 580 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7294 (mpp) REVERT: F 27 GLN cc_start: 0.8128 (pm20) cc_final: 0.7586 (pm20) outliers start: 52 outliers final: 20 residues processed: 252 average time/residue: 1.1004 time to fit residues: 314.1432 Evaluate side-chains 236 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 502 HIS H 86 ASN A 80 HIS A 196 ASN A 364 GLN B 80 HIS B 502 HIS F 35 ASN I 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.174812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130368 restraints weight = 22851.359| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.64 r_work: 0.3502 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17547 Z= 0.111 Angle : 0.527 7.007 23868 Z= 0.269 Chirality : 0.044 0.155 2547 Planarity : 0.004 0.046 3099 Dihedral : 4.344 15.808 2337 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.04 % Allowed : 17.76 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2127 helix: -1.98 (0.48), residues: 99 sheet: -0.58 (0.17), residues: 927 loop : -0.54 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.015 0.001 HIS A 80 PHE 0.009 0.001 PHE F 93 TYR 0.011 0.001 TYR C 203 ARG 0.009 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 493) hydrogen bonds : angle 5.88170 ( 1236) SS BOND : bond 0.00387 ( 9) SS BOND : angle 0.91003 ( 18) covalent geometry : bond 0.00252 (17538) covalent geometry : angle 0.52673 (23850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 1.749 Fit side-chains REVERT: C 103 ASP cc_start: 0.7573 (p0) cc_final: 0.7362 (p0) REVERT: C 133 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6643 (tt0) REVERT: C 305 ASP cc_start: 0.7732 (t0) cc_final: 0.7072 (t0) REVERT: C 365 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7800 (pttm) REVERT: C 498 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.5524 (mpt) REVERT: D 91 TYR cc_start: 0.8055 (m-80) cc_final: 0.7739 (m-80) REVERT: H 38 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7755 (ptm160) REVERT: H 46 GLU cc_start: 0.7913 (tt0) cc_final: 0.7214 (mt-10) REVERT: A 133 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: A 230 GLN cc_start: 0.8063 (tp40) cc_final: 0.7791 (tp-100) REVERT: A 456 MET cc_start: 0.0850 (ppp) cc_final: -0.1013 (ppp) REVERT: A 466 MET cc_start: 0.7132 (ttt) cc_final: 0.6904 (tpt) REVERT: A 498 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6579 (mpt) REVERT: G 38 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7978 (ptp90) REVERT: G 84 GLN cc_start: 0.7880 (tp40) cc_final: 0.7581 (tp40) REVERT: B 133 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: B 230 GLN cc_start: 0.8151 (tp40) cc_final: 0.7845 (tp-100) REVERT: B 466 MET cc_start: 0.6967 (tpt) cc_final: 0.6666 (mmm) REVERT: B 498 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.5310 (mpt) REVERT: B 553 PHE cc_start: 0.5877 (OUTLIER) cc_final: 0.5587 (m-10) REVERT: B 580 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: F 27 GLN cc_start: 0.8037 (pm20) cc_final: 0.7507 (pm20) REVERT: F 111 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.5445 (tppt) REVERT: I 38 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7868 (ttm170) outliers start: 57 outliers final: 20 residues processed: 255 average time/residue: 1.0811 time to fit residues: 312.4418 Evaluate side-chains 243 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 111 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 160 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 203 optimal weight: 0.1980 chunk 33 optimal weight: 0.0980 chunk 140 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 200 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 502 HIS H 86 ASN A 80 HIS A 364 GLN G 86 ASN B 80 HIS B 475 ASN B 502 HIS F 35 ASN F 54 GLN I 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133117 restraints weight = 22755.213| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.64 r_work: 0.3537 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17547 Z= 0.089 Angle : 0.504 6.365 23868 Z= 0.257 Chirality : 0.044 0.207 2547 Planarity : 0.004 0.042 3099 Dihedral : 4.132 16.588 2337 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.61 % Allowed : 17.49 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % 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: -0.83 (0.18), residues: 2127 helix: -1.66 (0.50), residues: 99 sheet: -0.43 (0.17), residues: 918 loop : -0.42 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 61 HIS 0.015 0.001 HIS A 80 PHE 0.009 0.001 PHE F 93 TYR 0.011 0.001 TYR C 203 ARG 0.009 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.02450 ( 493) hydrogen bonds : angle 5.60427 ( 1236) SS BOND : bond 0.00362 ( 9) SS BOND : angle 0.80942 ( 18) covalent geometry : bond 0.00200 (17538) covalent geometry : angle 0.50419 (23850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 2.018 Fit side-chains REVERT: C 133 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: C 305 ASP cc_start: 0.7563 (t0) cc_final: 0.7051 (t0) REVERT: C 365 LYS cc_start: 0.7967 (ptmt) cc_final: 0.7738 (ptpp) REVERT: H 46 GLU cc_start: 0.7865 (tt0) cc_final: 0.7208 (mt-10) REVERT: A 181 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: A 203 TYR cc_start: 0.6956 (p90) cc_final: 0.6751 (p90) REVERT: A 230 GLN cc_start: 0.7989 (tp40) cc_final: 0.7761 (tp-100) REVERT: A 466 MET cc_start: 0.7119 (ttt) cc_final: 0.6917 (tpt) REVERT: A 498 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6497 (mpt) REVERT: E 27 GLN cc_start: 0.8259 (pm20) cc_final: 0.7660 (pm20) REVERT: E 57 ASN cc_start: 0.7709 (m110) cc_final: 0.7319 (m110) REVERT: G 84 GLN cc_start: 0.7881 (tp40) cc_final: 0.7521 (tp40) REVERT: B 104 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6304 (ptt) REVERT: B 133 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6673 (tt0) REVERT: B 230 GLN cc_start: 0.8129 (tp40) cc_final: 0.7830 (tp-100) REVERT: B 409 ASN cc_start: 0.8336 (m110) cc_final: 0.8109 (m110) REVERT: B 466 MET cc_start: 0.6951 (tpt) cc_final: 0.6676 (mmm) REVERT: B 479 GLN cc_start: 0.8352 (mt0) cc_final: 0.7906 (mm110) REVERT: B 498 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.5103 (mpt) REVERT: B 553 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5580 (m-10) REVERT: B 580 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7145 (mpp) REVERT: F 27 GLN cc_start: 0.7953 (pm20) cc_final: 0.7411 (pm20) REVERT: I 85 MET cc_start: 0.8236 (mtp) cc_final: 0.7932 (mtp) REVERT: I 89 ARG cc_start: 0.6831 (mtm110) cc_final: 0.6571 (mtm-85) outliers start: 49 outliers final: 20 residues processed: 247 average time/residue: 1.1679 time to fit residues: 325.9156 Evaluate side-chains 239 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 315 ASN C 502 HIS H 86 ASN A 80 HIS A 364 GLN B 80 HIS B 502 HIS B 503 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124249 restraints weight = 22605.525| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.69 r_work: 0.3438 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17547 Z= 0.253 Angle : 0.635 8.240 23868 Z= 0.326 Chirality : 0.048 0.191 2547 Planarity : 0.005 0.046 3099 Dihedral : 4.899 19.011 2337 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.51 % Allowed : 18.61 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2127 helix: -1.94 (0.42), residues: 117 sheet: -0.59 (0.17), residues: 912 loop : -0.60 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 61 HIS 0.016 0.001 HIS C 80 PHE 0.013 0.002 PHE F 93 TYR 0.013 0.002 TYR H 97 ARG 0.011 0.001 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 493) hydrogen bonds : angle 6.31711 ( 1236) SS BOND : bond 0.00445 ( 9) SS BOND : angle 1.18568 ( 18) covalent geometry : bond 0.00598 (17538) covalent geometry : angle 0.63481 (23850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.873 Fit side-chains REVERT: C 90 LEU cc_start: 0.7145 (mp) cc_final: 0.6907 (mp) REVERT: C 133 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6710 (tt0) REVERT: C 305 ASP cc_start: 0.7665 (t0) cc_final: 0.7022 (t0) REVERT: C 466 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6861 (tpt) REVERT: D 91 TYR cc_start: 0.8140 (m-80) cc_final: 0.7821 (m-80) REVERT: H 46 GLU cc_start: 0.7825 (tt0) cc_final: 0.7058 (mt-10) REVERT: A 230 GLN cc_start: 0.8166 (tp40) cc_final: 0.7803 (tp-100) REVERT: A 498 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6596 (mpt) REVERT: G 84 GLN cc_start: 0.8023 (tp40) cc_final: 0.7683 (tp40) REVERT: B 104 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6318 (ptt) REVERT: B 133 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6666 (tt0) REVERT: B 230 GLN cc_start: 0.8225 (tp40) cc_final: 0.7917 (tp-100) REVERT: B 244 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8339 (p0) REVERT: B 466 MET cc_start: 0.7053 (tpt) cc_final: 0.6758 (mmm) REVERT: B 580 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7258 (mpp) REVERT: I 38 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7919 (ttm170) outliers start: 47 outliers final: 17 residues processed: 250 average time/residue: 1.1819 time to fit residues: 332.9986 Evaluate side-chains 244 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 128 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 64 optimal weight: 0.0470 chunk 130 optimal weight: 2.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 502 HIS H 86 ASN A 80 HIS A 364 GLN A 502 HIS G 86 ASN B 80 HIS B 502 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127346 restraints weight = 22820.878| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.63 r_work: 0.3466 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17547 Z= 0.159 Angle : 0.577 7.667 23868 Z= 0.295 Chirality : 0.046 0.182 2547 Planarity : 0.004 0.050 3099 Dihedral : 4.659 16.880 2337 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.19 % Allowed : 19.15 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2127 helix: -1.77 (0.44), residues: 117 sheet: -0.60 (0.17), residues: 912 loop : -0.56 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 61 HIS 0.016 0.001 HIS A 80 PHE 0.010 0.001 PHE F 93 TYR 0.011 0.001 TYR B 203 ARG 0.013 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 493) hydrogen bonds : angle 6.13688 ( 1236) SS BOND : bond 0.00419 ( 9) SS BOND : angle 0.97789 ( 18) covalent geometry : bond 0.00371 (17538) covalent geometry : angle 0.57696 (23850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 2.038 Fit side-chains REVERT: C 133 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: C 305 ASP cc_start: 0.7705 (t0) cc_final: 0.7042 (t0) REVERT: D 91 TYR cc_start: 0.8105 (m-80) cc_final: 0.7766 (m-80) REVERT: H 46 GLU cc_start: 0.7780 (tt0) cc_final: 0.7070 (mt-10) REVERT: H 95 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.6992 (mmm160) REVERT: A 230 GLN cc_start: 0.8115 (tp40) cc_final: 0.7833 (tp-100) REVERT: A 498 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.6509 (mpt) REVERT: A 550 ILE cc_start: 0.6658 (mm) cc_final: 0.6431 (mm) REVERT: E 111 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5016 (tptm) REVERT: G 84 GLN cc_start: 0.7975 (tp40) cc_final: 0.7668 (tp40) REVERT: B 104 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6213 (ptt) REVERT: B 133 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: B 230 GLN cc_start: 0.8200 (tp40) cc_final: 0.7901 (tp-100) REVERT: B 244 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8280 (p0) REVERT: B 466 MET cc_start: 0.7021 (tpt) cc_final: 0.6697 (mmm) REVERT: B 498 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.5391 (mpt) REVERT: B 580 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7242 (mpp) REVERT: F 27 GLN cc_start: 0.8140 (pm20) cc_final: 0.7549 (pm20) outliers start: 41 outliers final: 22 residues processed: 239 average time/residue: 1.2018 time to fit residues: 324.6158 Evaluate side-chains 246 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 144 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS H 86 ASN A 80 HIS A 364 GLN A 502 HIS G 86 ASN B 80 HIS B 502 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128214 restraints weight = 22814.787| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.71 r_work: 0.3481 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17547 Z= 0.131 Angle : 0.553 7.299 23868 Z= 0.283 Chirality : 0.045 0.176 2547 Planarity : 0.004 0.055 3099 Dihedral : 4.463 16.353 2337 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.87 % Allowed : 19.52 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2127 helix: -2.07 (0.47), residues: 99 sheet: -0.63 (0.17), residues: 921 loop : -0.50 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 61 HIS 0.015 0.001 HIS A 80 PHE 0.010 0.001 PHE E 93 TYR 0.011 0.001 TYR C 203 ARG 0.013 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.02741 ( 493) hydrogen bonds : angle 5.94686 ( 1236) SS BOND : bond 0.00409 ( 9) SS BOND : angle 0.94896 ( 18) covalent geometry : bond 0.00303 (17538) covalent geometry : angle 0.55219 (23850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 1.851 Fit side-chains REVERT: C 76 LYS cc_start: 0.7847 (mppt) cc_final: 0.7596 (mppt) REVERT: C 103 ASP cc_start: 0.7592 (p0) cc_final: 0.7337 (p0) REVERT: C 133 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: C 305 ASP cc_start: 0.7721 (t0) cc_final: 0.7063 (t0) REVERT: C 498 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.5331 (mpt) REVERT: H 46 GLU cc_start: 0.7870 (tt0) cc_final: 0.7217 (mt-10) REVERT: H 95 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7021 (mmm160) REVERT: A 230 GLN cc_start: 0.8076 (tp40) cc_final: 0.7761 (tp-100) REVERT: A 498 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6572 (mpt) REVERT: A 550 ILE cc_start: 0.6609 (mm) cc_final: 0.6396 (mm) REVERT: G 84 GLN cc_start: 0.7987 (tp40) cc_final: 0.7708 (tp40) REVERT: B 104 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6280 (ptt) REVERT: B 133 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: B 230 GLN cc_start: 0.8194 (tp40) cc_final: 0.7910 (tp-100) REVERT: B 244 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8259 (p0) REVERT: B 466 MET cc_start: 0.6993 (tpt) cc_final: 0.6665 (mmm) REVERT: B 498 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.5384 (mpt) REVERT: B 580 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: F 27 GLN cc_start: 0.8099 (pm20) cc_final: 0.7538 (pm20) outliers start: 35 outliers final: 20 residues processed: 235 average time/residue: 1.1749 time to fit residues: 310.8897 Evaluate side-chains 246 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 60 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 169 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS H 86 ASN A 80 HIS A 364 GLN A 502 HIS G 86 ASN B 80 HIS B 502 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.171152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126546 restraints weight = 22732.158| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.62 r_work: 0.3456 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17547 Z= 0.183 Angle : 0.593 7.704 23868 Z= 0.303 Chirality : 0.047 0.172 2547 Planarity : 0.005 0.057 3099 Dihedral : 4.688 17.610 2337 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.13 % Allowed : 19.52 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2127 helix: -1.73 (0.44), residues: 117 sheet: -0.67 (0.17), residues: 927 loop : -0.51 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 61 HIS 0.014 0.001 HIS A 80 PHE 0.010 0.001 PHE F 93 TYR 0.011 0.001 TYR H 97 ARG 0.013 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 493) hydrogen bonds : angle 6.14124 ( 1236) SS BOND : bond 0.00424 ( 9) SS BOND : angle 1.04235 ( 18) covalent geometry : bond 0.00431 (17538) covalent geometry : angle 0.59265 (23850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13826.29 seconds wall clock time: 238 minutes 24.70 seconds (14304.70 seconds total)