Starting phenix.real_space_refine on Sun Aug 24 04:39:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3o_38893/08_2025/8y3o_38893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3o_38893/08_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_38893/08_2025/8y3o_38893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3o_38893/08_2025/8y3o_38893.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3o_38893/08_2025/8y3o_38893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3o_38893/08_2025/8y3o_38893.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.58, per 1000 atoms: 0.27 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: 1.19 Conformation dependent library (CDL) restraints added in 846.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 3.16 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.140 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.000 ARG F 65 TYR 0.021 0.002 TYR G 62 PHE 0.019 0.001 PHE B 467 TRP 0.027 0.001 TRP E 61 HIS 0.013 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00346 (17538) covalent geometry : angle 0.74501 (23850) SS BOND : bond 0.00564 ( 9) SS BOND : angle 0.87284 ( 18) hydrogen bonds : bond 0.11561 ( 493) hydrogen bonds : angle 7.09858 ( 1236) *********************** 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 : 0.570 Fit side-chains REVERT: A 221 MET cc_start: 0.6921 (tpt) cc_final: 0.6691 (tpt) REVERT: E 86 ASP cc_start: 0.8440 (m-30) cc_final: 0.8188 (m-30) 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: 0.6327 time to fit residues: 177.0568 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 : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 H 86 ASN 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 502 HIS I 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135098 restraints weight = 22783.246| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.64 r_work: 0.3559 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17547 Z= 0.104 Angle : 0.517 6.866 23868 Z= 0.265 Chirality : 0.044 0.146 2547 Planarity : 0.005 0.073 3099 Dihedral : 4.410 17.424 2337 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.07 % Allowed : 8.64 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.18), residues: 2127 helix: -1.83 (0.44), residues: 114 sheet: -0.28 (0.17), residues: 897 loop : -0.62 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 24 TYR 0.009 0.001 TYR B 203 PHE 0.011 0.001 PHE A 137 TRP 0.010 0.001 TRP E 61 HIS 0.017 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00229 (17538) covalent geometry : angle 0.51666 (23850) SS BOND : bond 0.00365 ( 9) SS BOND : angle 0.90212 ( 18) hydrogen bonds : bond 0.02814 ( 493) hydrogen bonds : angle 5.95884 ( 1236) *********************** 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 237 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.677 Fit side-chains REVERT: C 221 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6149 (tpp) REVERT: C 456 MET cc_start: 0.0077 (ppp) cc_final: -0.0912 (ppp) REVERT: H 46 GLU cc_start: 0.7975 (tt0) cc_final: 0.7536 (mt-10) REVERT: A 466 MET cc_start: 0.7360 (ttt) cc_final: 0.6821 (tpt) REVERT: E 27 GLN cc_start: 0.7957 (pm20) cc_final: 0.7556 (pm20) REVERT: E 65 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6435 (ptt180) REVERT: G 38 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7050 (ptt180) REVERT: B 466 MET cc_start: 0.6546 (tpt) cc_final: 0.6268 (mmm) outliers start: 20 outliers final: 9 residues processed: 228 average time/residue: 0.5681 time to fit residues: 146.0124 Evaluate side-chains 210 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 118 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain E residue 65 ARG 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 F residue 30 GLU 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 35 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 120 optimal weight: 0.0570 chunk 153 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 114 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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 G 86 ASN B 80 HIS B 502 HIS I 84 GLN I 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135502 restraints weight = 22966.279| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.66 r_work: 0.3569 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17547 Z= 0.091 Angle : 0.494 6.248 23868 Z= 0.251 Chirality : 0.044 0.146 2547 Planarity : 0.004 0.056 3099 Dihedral : 4.136 16.073 2337 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.81 % Allowed : 10.03 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.18), residues: 2127 helix: -1.45 (0.45), residues: 114 sheet: -0.11 (0.17), residues: 882 loop : -0.53 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 24 TYR 0.013 0.001 TYR H 61 PHE 0.008 0.001 PHE A 137 TRP 0.009 0.001 TRP G 47 HIS 0.015 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00202 (17538) covalent geometry : angle 0.49317 (23850) SS BOND : bond 0.00381 ( 9) SS BOND : angle 0.85840 ( 18) hydrogen bonds : bond 0.02582 ( 493) hydrogen bonds : angle 5.63771 ( 1236) *********************** 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 249 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.686 Fit side-chains REVERT: C 221 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6098 (tpp) REVERT: C 305 ASP cc_start: 0.7374 (t0) cc_final: 0.7066 (t0) REVERT: C 498 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.5686 (mpt) REVERT: D 27 GLN cc_start: 0.8043 (pm20) cc_final: 0.6864 (pm20) REVERT: H 38 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7871 (ptp90) REVERT: H 46 GLU cc_start: 0.7992 (tt0) cc_final: 0.7489 (mt-10) REVERT: A 133 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 203 TYR cc_start: 0.7144 (p90) cc_final: 0.6924 (p90) REVERT: A 230 GLN cc_start: 0.8024 (tp40) cc_final: 0.7788 (tp-100) REVERT: A 409 ASN cc_start: 0.8332 (m110) cc_final: 0.8064 (m110) REVERT: A 466 MET cc_start: 0.7394 (ttt) cc_final: 0.6979 (tpt) REVERT: A 498 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.5478 (mpt) REVERT: E 27 GLN cc_start: 0.7911 (pm20) cc_final: 0.7528 (pm20) REVERT: E 57 ASN cc_start: 0.7823 (m110) cc_final: 0.7418 (m110) REVERT: E 58 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7917 (mtm180) REVERT: E 97 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: G 38 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7971 (ptm160) REVERT: B 466 MET cc_start: 0.6549 (tpt) cc_final: 0.6329 (mmm) REVERT: F 65 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7368 (ptt-90) REVERT: I 20 LEU cc_start: 0.8031 (mp) cc_final: 0.7659 (mt) outliers start: 34 outliers final: 9 residues processed: 228 average time/residue: 0.6059 time to fit residues: 155.0544 Evaluate side-chains 212 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET 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 38 ARG 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 498 MET Chi-restraints excluded: chain E residue 97 GLN 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 F residue 30 GLU Chi-restraints excluded: chain F residue 89 VAL 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 91 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 76 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 0.0170 overall best weight: 1.0820 ------------------------------------------------------------------------------- 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 76 ASN H 86 ASN A 80 HIS G 86 ASN B 80 HIS B 230 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.177247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133097 restraints weight = 22669.096| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.64 r_work: 0.3526 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17547 Z= 0.120 Angle : 0.512 7.291 23868 Z= 0.262 Chirality : 0.044 0.149 2547 Planarity : 0.004 0.050 3099 Dihedral : 4.217 16.042 2337 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.19 % Allowed : 11.79 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.18), residues: 2127 helix: -1.36 (0.44), residues: 114 sheet: -0.11 (0.17), residues: 879 loop : -0.48 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 24 TYR 0.009 0.001 TYR B 203 PHE 0.008 0.001 PHE A 161 TRP 0.009 0.001 TRP H 47 HIS 0.015 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00275 (17538) covalent geometry : angle 0.51170 (23850) SS BOND : bond 0.00344 ( 9) SS BOND : angle 0.83627 ( 18) hydrogen bonds : bond 0.02694 ( 493) hydrogen bonds : angle 5.71697 ( 1236) *********************** 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 255 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.687 Fit side-chains REVERT: C 133 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: C 221 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6151 (tpp) REVERT: H 38 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7868 (ptm160) REVERT: H 46 GLU cc_start: 0.7983 (tt0) cc_final: 0.7469 (mt-10) REVERT: H 100 GLU cc_start: 0.8293 (tt0) cc_final: 0.7910 (tt0) REVERT: A 133 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: A 203 TYR cc_start: 0.7253 (p90) cc_final: 0.6937 (p90) REVERT: A 230 GLN cc_start: 0.8135 (tp40) cc_final: 0.7888 (tp-100) REVERT: A 498 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.5742 (mpt) REVERT: E 27 GLN cc_start: 0.7995 (pm20) cc_final: 0.7617 (pm20) REVERT: E 54 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: E 57 ASN cc_start: 0.7905 (m110) cc_final: 0.7546 (m110) REVERT: E 58 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7890 (mtm180) REVERT: G 38 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7993 (ptp90) REVERT: B 133 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: B 244 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 409 ASN cc_start: 0.8284 (m110) cc_final: 0.8067 (m110) REVERT: B 466 MET cc_start: 0.6817 (tpt) cc_final: 0.6588 (mmm) REVERT: B 498 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.5208 (mpt) REVERT: B 553 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5750 (m-10) REVERT: F 27 GLN cc_start: 0.7886 (pm20) cc_final: 0.7546 (pm20) REVERT: I 20 LEU cc_start: 0.8144 (mp) cc_final: 0.7804 (mp) outliers start: 41 outliers final: 14 residues processed: 232 average time/residue: 0.5499 time to fit residues: 143.9478 Evaluate side-chains 227 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 620 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain H residue 38 ARG 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 498 MET Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 54 GLN 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 244 ASN 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 F residue 30 GLU Chi-restraints excluded: chain F residue 89 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 18 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 30 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131410 restraints weight = 22676.351| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.65 r_work: 0.3516 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17547 Z= 0.122 Angle : 0.515 7.351 23868 Z= 0.262 Chirality : 0.044 0.149 2547 Planarity : 0.004 0.043 3099 Dihedral : 4.235 16.211 2337 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.24 % Allowed : 13.44 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.18), residues: 2127 helix: -1.32 (0.45), residues: 114 sheet: -0.12 (0.17), residues: 876 loop : -0.44 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 24 TYR 0.009 0.001 TYR B 203 PHE 0.008 0.001 PHE F 93 TRP 0.009 0.001 TRP H 47 HIS 0.015 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00281 (17538) covalent geometry : angle 0.51496 (23850) SS BOND : bond 0.00350 ( 9) SS BOND : angle 0.85378 ( 18) hydrogen bonds : bond 0.02673 ( 493) hydrogen bonds : angle 5.74725 ( 1236) *********************** 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 262 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.609 Fit side-chains REVERT: C 133 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: C 221 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6156 (tpp) REVERT: C 305 ASP cc_start: 0.7567 (t0) cc_final: 0.6891 (t0) REVERT: C 498 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.5568 (mpt) REVERT: H 38 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7926 (ptp90) REVERT: H 46 GLU cc_start: 0.7938 (tt0) cc_final: 0.7429 (mt-10) REVERT: H 100 GLU cc_start: 0.8319 (tt0) cc_final: 0.7979 (tt0) REVERT: A 133 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6742 (tt0) REVERT: A 203 TYR cc_start: 0.7284 (p90) cc_final: 0.6939 (p90) REVERT: A 230 GLN cc_start: 0.8049 (tp40) cc_final: 0.7810 (tp-100) REVERT: A 498 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.5830 (mpt) REVERT: E 27 GLN cc_start: 0.8142 (pm20) cc_final: 0.7734 (pm20) REVERT: E 54 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: E 57 ASN cc_start: 0.7961 (m110) cc_final: 0.7607 (m110) REVERT: G 38 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7994 (ptp90) REVERT: B 133 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: B 244 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8101 (p0) REVERT: B 466 MET cc_start: 0.6864 (tpt) cc_final: 0.6599 (mmm) REVERT: B 580 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7228 (mpp) REVERT: F 27 GLN cc_start: 0.8010 (pm20) cc_final: 0.7404 (pm20) REVERT: I 20 LEU cc_start: 0.7989 (mp) cc_final: 0.7613 (mt) outliers start: 42 outliers final: 15 residues processed: 236 average time/residue: 0.4854 time to fit residues: 129.0609 Evaluate side-chains 234 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 498 MET Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 620 THR 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 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 A residue 580 MET Chi-restraints excluded: chain E residue 54 GLN 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 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 F residue 30 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 148 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 86 ASN A 80 HIS A 483 GLN G 86 ASN B 80 HIS B 483 GLN B 502 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126439 restraints weight = 22637.937| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.61 r_work: 0.3455 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17547 Z= 0.221 Angle : 0.606 8.946 23868 Z= 0.310 Chirality : 0.047 0.205 2547 Planarity : 0.005 0.041 3099 Dihedral : 4.751 17.608 2337 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.67 % Allowed : 14.35 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.18), residues: 2127 helix: -2.20 (0.45), residues: 99 sheet: -0.36 (0.17), residues: 897 loop : -0.56 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 24 TYR 0.014 0.002 TYR H 96 PHE 0.011 0.001 PHE F 93 TRP 0.011 0.002 TRP C 336 HIS 0.016 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00519 (17538) covalent geometry : angle 0.60577 (23850) SS BOND : bond 0.00392 ( 9) SS BOND : angle 1.02015 ( 18) hydrogen bonds : bond 0.03298 ( 493) hydrogen bonds : angle 6.30020 ( 1236) *********************** 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 278 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.684 Fit side-chains REVERT: C 133 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: C 221 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6078 (tpp) REVERT: C 305 ASP cc_start: 0.7694 (t0) cc_final: 0.7014 (t0) REVERT: H 38 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7286 (ptt180) REVERT: H 46 GLU cc_start: 0.7876 (tt0) cc_final: 0.7335 (mt-10) REVERT: H 92 ASP cc_start: 0.8021 (m-30) cc_final: 0.7730 (m-30) REVERT: A 133 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: A 203 TYR cc_start: 0.7437 (p90) cc_final: 0.6958 (p90) REVERT: A 230 GLN cc_start: 0.8137 (tp40) cc_final: 0.7832 (tp-100) REVERT: E 111 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5129 (tptm) REVERT: G 38 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7140 (ptt180) REVERT: B 104 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6457 (ptt) REVERT: B 133 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: B 244 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8156 (p0) REVERT: B 466 MET cc_start: 0.7041 (tpt) cc_final: 0.6772 (mmm) REVERT: B 580 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7296 (mpp) REVERT: F 27 GLN cc_start: 0.8035 (pm20) cc_final: 0.7300 (pm20) outliers start: 50 outliers final: 16 residues processed: 252 average time/residue: 0.5465 time to fit residues: 155.0672 Evaluate side-chains 242 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 466 MET 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 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 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 104 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR 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 I residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 128 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 0.0040 chunk 189 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.173812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129255 restraints weight = 22734.141| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.64 r_work: 0.3486 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17547 Z= 0.130 Angle : 0.542 7.659 23868 Z= 0.276 Chirality : 0.045 0.199 2547 Planarity : 0.004 0.044 3099 Dihedral : 4.430 16.289 2337 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.19 % Allowed : 15.41 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.18), residues: 2127 helix: -2.07 (0.47), residues: 99 sheet: -0.30 (0.17), residues: 891 loop : -0.50 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 24 TYR 0.009 0.001 TYR C 203 PHE 0.009 0.001 PHE F 93 TRP 0.011 0.001 TRP C 336 HIS 0.015 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00301 (17538) covalent geometry : angle 0.54157 (23850) SS BOND : bond 0.00382 ( 9) SS BOND : angle 0.88664 ( 18) hydrogen bonds : bond 0.02768 ( 493) hydrogen bonds : angle 6.00096 ( 1236) *********************** 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 268 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.620 Fit side-chains REVERT: C 133 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: C 221 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6200 (tpp) REVERT: C 305 ASP cc_start: 0.7692 (t0) cc_final: 0.7023 (t0) REVERT: H 46 GLU cc_start: 0.7969 (tt0) cc_final: 0.7412 (mt-10) REVERT: A 133 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: A 203 TYR cc_start: 0.7276 (p90) cc_final: 0.6905 (p90) REVERT: A 230 GLN cc_start: 0.8078 (tp40) cc_final: 0.7818 (tp-100) REVERT: A 498 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.5814 (mpt) REVERT: E 27 GLN cc_start: 0.8322 (pm20) cc_final: 0.7384 (pm20) REVERT: G 38 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7927 (ptm160) REVERT: B 104 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6382 (ptt) REVERT: B 133 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: B 230 GLN cc_start: 0.8205 (tp40) cc_final: 0.7939 (tp-100) REVERT: B 466 MET cc_start: 0.7039 (tpt) cc_final: 0.6799 (mmm) REVERT: B 498 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.5404 (mpt) REVERT: B 580 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7279 (mpp) REVERT: F 27 GLN cc_start: 0.7994 (pm20) cc_final: 0.7468 (pm20) REVERT: I 20 LEU cc_start: 0.8264 (mp) cc_final: 0.8019 (mp) outliers start: 41 outliers final: 18 residues processed: 241 average time/residue: 0.5226 time to fit residues: 142.2015 Evaluate side-chains 240 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 466 MET Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 553 PHE 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 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 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 104 MET Chi-restraints excluded: chain B residue 133 GLN 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 B residue 583 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS H 76 ASN H 86 ASN A 80 HIS G 86 ASN B 80 HIS B 502 HIS F 35 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132281 restraints weight = 22667.718| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.62 r_work: 0.3514 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17547 Z= 0.109 Angle : 0.525 7.344 23868 Z= 0.266 Chirality : 0.045 0.184 2547 Planarity : 0.004 0.041 3099 Dihedral : 4.230 15.726 2337 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.19 % Allowed : 16.21 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 2127 helix: -1.37 (0.45), residues: 114 sheet: -0.27 (0.17), residues: 894 loop : -0.35 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 24 TYR 0.009 0.001 TYR B 203 PHE 0.009 0.001 PHE E 93 TRP 0.010 0.001 TRP H 47 HIS 0.015 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00250 (17538) covalent geometry : angle 0.52458 (23850) SS BOND : bond 0.00387 ( 9) SS BOND : angle 0.86746 ( 18) hydrogen bonds : bond 0.02600 ( 493) hydrogen bonds : angle 5.75641 ( 1236) *********************** 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 272 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.854 Fit side-chains REVERT: C 103 ASP cc_start: 0.7689 (p0) cc_final: 0.7441 (p0) REVERT: C 133 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: C 221 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6211 (tpp) REVERT: C 305 ASP cc_start: 0.7676 (t0) cc_final: 0.7006 (t0) REVERT: C 498 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.5383 (mpt) REVERT: H 46 GLU cc_start: 0.7933 (tt0) cc_final: 0.7376 (mt-10) REVERT: A 203 TYR cc_start: 0.7198 (p90) cc_final: 0.6887 (p90) REVERT: A 230 GLN cc_start: 0.8037 (tp40) cc_final: 0.7773 (tp-100) REVERT: A 466 MET cc_start: 0.7131 (ttt) cc_final: 0.6865 (tpt) REVERT: A 498 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.5878 (mpt) REVERT: A 550 ILE cc_start: 0.6567 (mm) cc_final: 0.6353 (mm) REVERT: E 54 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: G 38 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7962 (ptm160) REVERT: G 84 GLN cc_start: 0.7927 (tp40) cc_final: 0.7631 (tp40) REVERT: B 104 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6296 (ptt) REVERT: B 230 GLN cc_start: 0.8158 (tp40) cc_final: 0.7900 (tp-100) REVERT: B 466 MET cc_start: 0.6971 (tpt) cc_final: 0.6739 (mmm) REVERT: B 498 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.5214 (mpt) REVERT: B 553 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.5605 (m-10) REVERT: B 580 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7150 (mpp) REVERT: F 27 GLN cc_start: 0.7964 (pm20) cc_final: 0.7418 (pm20) REVERT: I 20 LEU cc_start: 0.7924 (mp) cc_final: 0.7601 (mt) REVERT: I 38 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7783 (ttm170) outliers start: 41 outliers final: 19 residues processed: 246 average time/residue: 0.5543 time to fit residues: 153.5035 Evaluate side-chains 245 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 466 MET 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 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 E residue 54 GLN 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 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 I residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 G 86 ASN B 80 HIS B 502 HIS F 54 GLN F 94 GLN I 86 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131156 restraints weight = 22739.283| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.65 r_work: 0.3514 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2010 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= 0.115 Angle : 0.529 7.310 23868 Z= 0.269 Chirality : 0.045 0.176 2547 Planarity : 0.004 0.047 3099 Dihedral : 4.219 15.818 2337 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.24 % Allowed : 16.37 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2127 helix: -1.20 (0.46), residues: 114 sheet: -0.30 (0.17), residues: 900 loop : -0.30 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 24 TYR 0.009 0.001 TYR B 203 PHE 0.008 0.001 PHE E 93 TRP 0.009 0.001 TRP H 47 HIS 0.015 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00265 (17538) covalent geometry : angle 0.52858 (23850) SS BOND : bond 0.00381 ( 9) SS BOND : angle 0.86719 ( 18) hydrogen bonds : bond 0.02627 ( 493) hydrogen bonds : angle 5.71118 ( 1236) *********************** 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 261 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.711 Fit side-chains REVERT: C 103 ASP cc_start: 0.7642 (p0) cc_final: 0.7418 (p0) REVERT: C 133 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: C 221 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6138 (tpp) REVERT: C 305 ASP cc_start: 0.7773 (t0) cc_final: 0.7093 (t0) REVERT: C 498 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.5423 (mpt) REVERT: H 46 GLU cc_start: 0.7877 (tt0) cc_final: 0.7330 (mt-10) REVERT: A 133 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: A 203 TYR cc_start: 0.7206 (p90) cc_final: 0.6890 (p90) REVERT: A 230 GLN cc_start: 0.8032 (tp40) cc_final: 0.7815 (tp-100) REVERT: A 456 MET cc_start: 0.0801 (ppp) cc_final: -0.1013 (ppp) REVERT: A 466 MET cc_start: 0.7136 (ttt) cc_final: 0.6888 (tpt) REVERT: A 498 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.5861 (mpt) REVERT: A 581 MET cc_start: 0.7529 (ttt) cc_final: 0.7218 (ttp) REVERT: E 54 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: G 38 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7963 (ptm160) REVERT: B 76 LYS cc_start: 0.7838 (mppt) cc_final: 0.7572 (mppt) REVERT: B 104 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6302 (ptt) REVERT: B 133 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: B 230 GLN cc_start: 0.8139 (tp40) cc_final: 0.7907 (tp-100) REVERT: B 466 MET cc_start: 0.6935 (tpt) cc_final: 0.6710 (mmm) REVERT: B 498 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.5252 (mpt) REVERT: B 553 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5576 (m-10) REVERT: B 580 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7173 (mpp) REVERT: F 27 GLN cc_start: 0.7963 (pm20) cc_final: 0.7412 (pm20) REVERT: I 20 LEU cc_start: 0.8006 (mp) cc_final: 0.7704 (mt) REVERT: I 38 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.8071 (ttp-170) outliers start: 42 outliers final: 19 residues processed: 235 average time/residue: 0.5287 time to fit residues: 139.4900 Evaluate side-chains 249 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 466 MET Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL 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 580 MET Chi-restraints excluded: chain E residue 54 GLN 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 133 GLN 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 I residue 93 THR 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 167 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 5 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 G 86 ASN B 80 HIS B 502 HIS I 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.177400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133342 restraints weight = 22653.899| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.64 r_work: 0.3541 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17547 Z= 0.095 Angle : 0.513 7.146 23868 Z= 0.260 Chirality : 0.044 0.164 2547 Planarity : 0.004 0.057 3099 Dihedral : 4.063 15.681 2337 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.92 % Allowed : 17.07 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.18), residues: 2127 helix: -1.06 (0.48), residues: 114 sheet: -0.29 (0.17), residues: 897 loop : -0.23 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 24 TYR 0.009 0.001 TYR B 203 PHE 0.008 0.001 PHE E 93 TRP 0.010 0.001 TRP H 47 HIS 0.015 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00218 (17538) covalent geometry : angle 0.51264 (23850) SS BOND : bond 0.00363 ( 9) SS BOND : angle 0.85101 ( 18) hydrogen bonds : bond 0.02456 ( 493) hydrogen bonds : angle 5.53521 ( 1236) ********************** 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 264 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.534 Fit side-chains REVERT: C 103 ASP cc_start: 0.7540 (p0) cc_final: 0.7337 (p0) REVERT: C 133 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: C 221 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6186 (tpp) REVERT: C 305 ASP cc_start: 0.7590 (t0) cc_final: 0.6936 (t0) REVERT: C 498 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.5046 (mpt) REVERT: H 46 GLU cc_start: 0.7927 (tt0) cc_final: 0.7424 (mt-10) REVERT: A 133 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: A 203 TYR cc_start: 0.7160 (p90) cc_final: 0.6900 (p90) REVERT: A 230 GLN cc_start: 0.7980 (tp40) cc_final: 0.7744 (tp-100) REVERT: A 456 MET cc_start: 0.0765 (ppp) cc_final: -0.1068 (ppp) REVERT: A 466 MET cc_start: 0.7118 (ttt) cc_final: 0.6878 (tpt) REVERT: A 498 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.5743 (mpt) REVERT: E 57 ASN cc_start: 0.7799 (m110) cc_final: 0.7359 (m110) REVERT: G 38 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (ptp90) REVERT: G 84 GLN cc_start: 0.7938 (tp40) cc_final: 0.7576 (tp40) REVERT: B 76 LYS cc_start: 0.7852 (mppt) cc_final: 0.7577 (mppt) REVERT: B 133 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: B 466 MET cc_start: 0.6927 (tpt) cc_final: 0.6670 (mmm) REVERT: B 498 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.5192 (mpt) REVERT: B 553 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.5604 (m-10) REVERT: B 580 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: F 27 GLN cc_start: 0.8027 (pm20) cc_final: 0.7499 (pm20) REVERT: I 38 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7768 (ttm170) outliers start: 36 outliers final: 18 residues processed: 240 average time/residue: 0.5236 time to fit residues: 141.1591 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN 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 466 MET Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL 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 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 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 I residue 93 THR 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 54 optimal weight: 0.3980 chunk 195 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 120 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.176560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132383 restraints weight = 22714.209| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.64 r_work: 0.3528 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17547 Z= 0.108 Angle : 0.523 8.187 23868 Z= 0.266 Chirality : 0.044 0.164 2547 Planarity : 0.004 0.059 3099 Dihedral : 4.114 16.061 2337 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 17.28 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2127 helix: -1.06 (0.47), residues: 114 sheet: -0.26 (0.17), residues: 900 loop : -0.21 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.014 0.001 TYR H 61 PHE 0.012 0.001 PHE D 75 TRP 0.010 0.001 TRP H 47 HIS 0.016 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00248 (17538) covalent geometry : angle 0.52272 (23850) SS BOND : bond 0.00369 ( 9) SS BOND : angle 0.81734 ( 18) hydrogen bonds : bond 0.02553 ( 493) hydrogen bonds : angle 5.54566 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6553.96 seconds wall clock time: 112 minutes 27.13 seconds (6747.13 seconds total)