Starting phenix.real_space_refine on Fri Sep 27 20:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3o_38893/09_2024/8y3o_38893.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3o_38893/09_2024/8y3o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3o_38893/09_2024/8y3o_38893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3o_38893/09_2024/8y3o_38893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3o_38893/09_2024/8y3o_38893.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3o_38893/09_2024/8y3o_38893.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10884 2.51 5 N 2925 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17058 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "D" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 906 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "G" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 906 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "F" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 906 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 10.40, per 1000 atoms: 0.61 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: 4.12 Conformation dependent library (CDL) restraints added in 2.2 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 43 sheets defined 9.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'C' and resid 129 through 133 removed outlier: 4.047A pdb=" N GLY C 132 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.567A pdb=" N LEU C 343 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 344' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 555 through 566 Proline residue: C 563 - end of helix Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.030A pdb=" N THR H 93 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.169A pdb=" N GLY A 132 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.532A pdb=" N LEU A 343 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 344' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 555 through 566 Proline residue: A 563 - end of helix Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 89 through 93 removed outlier: 4.031A pdb=" N THR G 93 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.097A pdb=" N GLY B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.555A pdb=" N LEU B 343 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 344' Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 555 through 566 Proline residue: B 563 - end of helix Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 89 through 93 removed outlier: 4.019A pdb=" N THR I 93 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 72 through 75 removed outlier: 5.489A pdb=" N ASN C 409 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE C 109 " --> pdb=" O ASN C 409 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 89 through 93 removed outlier: 4.112A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AA5, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.143A pdb=" N SER C 387 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER C 521 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER C 523 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 391 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 234 through 246 removed outlier: 5.363A pdb=" N ASN C 309 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 307 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 242 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP C 305 " --> pdb=" O LEU C 242 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 305 through 314 current: chain 'C' and resid 528 through 534 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 528 through 534 current: chain 'A' and resid 305 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 305 through 314 current: chain 'A' and resid 528 through 534 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 528 through 534 current: chain 'B' and resid 305 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 305 through 314 current: chain 'B' and resid 528 through 534 Processing sheet with id=AA8, first strand: chain 'C' and resid 436 through 439 Processing sheet with id=AA9, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'D' and resid 57 through 58 removed outlier: 6.501A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR D 53 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.745A pdb=" N VAL H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 72 through 75 removed outlier: 5.469A pdb=" N ASN A 409 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 109 " --> pdb=" O ASN A 409 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 89 through 93 removed outlier: 4.035A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AC1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AC2, first strand: chain 'A' and resid 153 through 158 removed outlier: 6.172A pdb=" N SER A 387 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER A 521 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 523 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 391 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AC4, first strand: chain 'A' and resid 436 through 439 Processing sheet with id=AC5, first strand: chain 'A' and resid 444 through 446 Processing sheet with id=AC6, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AC7, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AC9, first strand: chain 'E' and resid 57 through 58 removed outlier: 5.362A pdb=" N LEU E 50 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN E 41 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.765A pdb=" N VAL G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 72 through 75 removed outlier: 5.461A pdb=" N ASN B 409 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 109 " --> pdb=" O ASN B 409 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 89 through 93 removed outlier: 4.062A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AD6, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AD7, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.131A pdb=" N SER B 387 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER B 521 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER B 523 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 391 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 176 through 179 Processing sheet with id=AD9, first strand: chain 'B' and resid 436 through 439 Processing sheet with id=AE1, first strand: chain 'B' and resid 444 through 446 Processing sheet with id=AE2, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AE3, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'F' and resid 57 through 58 removed outlier: 5.340A pdb=" N LEU F 50 " --> pdb=" O GLN F 41 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN F 41 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.755A pdb=" N VAL I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY I 50 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 4.83 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 39.740 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.680 ------------------------------------------------------------------------------- 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 17538 Z= 0.228 Angle : 0.745 9.845 23850 Z= 0.394 Chirality : 0.051 0.279 2547 Planarity : 0.007 0.122 3099 Dihedral : 13.070 87.429 6342 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2127 helix: -2.30 (0.42), residues: 111 sheet: -0.45 (0.17), residues: 915 loop : -0.96 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 61 HIS 0.013 0.001 HIS B 80 PHE 0.019 0.001 PHE B 467 TYR 0.021 0.002 TYR G 62 ARG 0.009 0.000 ARG F 65 *********************** 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 fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.858 Fit side-chains REVERT: A 221 MET cc_start: 0.6921 (tpt) cc_final: 0.6691 (tpt) REVERT: B 148 THR cc_start: 0.7976 (p) cc_final: 0.7768 (p) REVERT: B 538 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6276 (mppt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 1.2430 time to fit residues: 351.6124 Evaluate side-chains 209 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 475 ASN C 502 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN B 80 HIS B 230 GLN B 475 ASN B 502 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17538 Z= 0.398 Angle : 0.658 9.458 23850 Z= 0.340 Chirality : 0.049 0.162 2547 Planarity : 0.006 0.077 3099 Dihedral : 5.147 18.750 2337 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.49 % Allowed : 10.03 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2127 helix: -2.78 (0.42), residues: 99 sheet: -0.46 (0.17), residues: 903 loop : -0.81 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 61 HIS 0.017 0.002 HIS C 80 PHE 0.015 0.002 PHE B 137 TYR 0.013 0.002 TYR G 96 ARG 0.008 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 2.072 Fit side-chains REVERT: C 221 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5297 (tpp) REVERT: D 109 GLU cc_start: 0.5675 (tp30) cc_final: 0.5146 (tp30) REVERT: H 100 GLU cc_start: 0.7727 (tt0) cc_final: 0.7393 (tt0) REVERT: E 111 LYS cc_start: 0.5586 (OUTLIER) cc_final: 0.5074 (tptm) REVERT: G 19 LYS cc_start: 0.8416 (tptt) cc_final: 0.8199 (tptm) REVERT: G 38 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6921 (ptt180) REVERT: B 244 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 409 ASN cc_start: 0.8217 (m110) cc_final: 0.7940 (m110) REVERT: B 466 MET cc_start: 0.6810 (tpt) cc_final: 0.6503 (mmm) REVERT: F 27 GLN cc_start: 0.7977 (pm20) cc_final: 0.7518 (pm20) REVERT: F 111 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.5301 (tppt) outliers start: 28 outliers final: 14 residues processed: 243 average time/residue: 1.1481 time to fit residues: 314.7202 Evaluate side-chains 227 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 192 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 230 GLN A 502 HIS G 86 ASN B 80 HIS B 230 GLN B 483 GLN B 502 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17538 Z= 0.182 Angle : 0.534 7.852 23850 Z= 0.274 Chirality : 0.045 0.152 2547 Planarity : 0.005 0.059 3099 Dihedral : 4.584 17.027 2337 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 13.12 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2127 helix: -2.43 (0.45), residues: 99 sheet: -0.41 (0.17), residues: 900 loop : -0.67 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 336 HIS 0.015 0.001 HIS A 80 PHE 0.008 0.001 PHE A 137 TYR 0.010 0.001 TYR B 203 ARG 0.007 0.000 ARG E 24 *********************** 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 267 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 1.955 Fit side-chains REVERT: C 221 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5527 (tpp) REVERT: C 305 ASP cc_start: 0.6981 (t0) cc_final: 0.6625 (t0) REVERT: C 498 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.5402 (mpt) REVERT: H 46 GLU cc_start: 0.7376 (tt0) cc_final: 0.7098 (mt-10) REVERT: H 100 GLU cc_start: 0.7687 (tt0) cc_final: 0.7374 (tt0) REVERT: A 133 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: A 498 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.5645 (mpt) REVERT: E 27 GLN cc_start: 0.7963 (pm20) cc_final: 0.7250 (pm20) REVERT: G 19 LYS cc_start: 0.8290 (tptt) cc_final: 0.8077 (tptm) REVERT: G 38 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7779 (ptm160) REVERT: B 466 MET cc_start: 0.6827 (tpt) cc_final: 0.6546 (mmm) REVERT: B 580 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6665 (mpp) REVERT: F 27 GLN cc_start: 0.7972 (pm20) cc_final: 0.7471 (pm20) outliers start: 37 outliers final: 13 residues processed: 245 average time/residue: 1.1190 time to fit residues: 309.9426 Evaluate side-chains 231 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 488 HIS C 502 HIS D 54 GLN H 86 ASN A 80 HIS A 230 GLN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 17538 Z= 0.556 Angle : 0.715 9.796 23850 Z= 0.369 Chirality : 0.051 0.168 2547 Planarity : 0.006 0.061 3099 Dihedral : 5.359 22.148 2337 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.47 % Allowed : 14.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2127 helix: -2.78 (0.35), residues: 135 sheet: -0.75 (0.16), residues: 963 loop : -0.72 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 336 HIS 0.015 0.002 HIS A 80 PHE 0.015 0.002 PHE F 93 TYR 0.024 0.002 TYR H 96 ARG 0.008 0.001 ARG E 24 *********************** 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 291 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 226 time to evaluate : 1.999 Fit side-chains REVERT: C 104 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6384 (ptt) REVERT: C 133 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6672 (tt0) REVERT: C 365 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7639 (ptpp) REVERT: C 391 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 498 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.5795 (mpt) REVERT: C 613 ASP cc_start: 0.7245 (m-30) cc_final: 0.6754 (t0) REVERT: D 43 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7459 (mmtm) REVERT: D 64 GLU cc_start: 0.7264 (tp30) cc_final: 0.6493 (mp0) REVERT: D 91 TYR cc_start: 0.7995 (m-80) cc_final: 0.7656 (m-80) REVERT: D 109 GLU cc_start: 0.5789 (tp30) cc_final: 0.5318 (tp30) REVERT: A 133 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: A 305 ASP cc_start: 0.6887 (t0) cc_final: 0.6626 (t0) REVERT: A 580 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6872 (mmt) REVERT: E 111 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.5194 (tptm) REVERT: G 38 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6969 (ptt180) REVERT: B 104 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6576 (ptt) REVERT: B 244 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8124 (p0) REVERT: B 466 MET cc_start: 0.7017 (tpt) cc_final: 0.6661 (mmm) REVERT: B 580 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6915 (mpp) REVERT: F 27 GLN cc_start: 0.8100 (pm20) cc_final: 0.7654 (pm20) outliers start: 65 outliers final: 23 residues processed: 262 average time/residue: 1.1231 time to fit residues: 333.5291 Evaluate side-chains 247 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 365 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 2 optimal weight: 0.0470 chunk 153 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 A 230 GLN A 483 GLN A 502 HIS G 86 ASN B 80 HIS B 230 GLN B 502 HIS F 35 ASN F 94 GLN I 84 GLN I 86 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17538 Z= 0.157 Angle : 0.530 7.264 23850 Z= 0.272 Chirality : 0.045 0.154 2547 Planarity : 0.004 0.048 3099 Dihedral : 4.534 17.637 2337 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.61 % Allowed : 16.69 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2127 helix: -2.29 (0.46), residues: 99 sheet: -0.62 (0.17), residues: 894 loop : -0.59 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 336 HIS 0.016 0.001 HIS A 80 PHE 0.008 0.001 PHE B 337 TYR 0.021 0.001 TYR A 203 ARG 0.010 0.000 ARG E 24 *********************** 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 276 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 2.084 Fit side-chains REVERT: C 133 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: D 91 TYR cc_start: 0.7942 (m-80) cc_final: 0.7633 (m-80) REVERT: H 46 GLU cc_start: 0.7524 (tt0) cc_final: 0.7033 (mt-10) REVERT: A 133 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 498 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.5964 (mpt) REVERT: G 38 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.6714 (ptt180) REVERT: B 133 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: B 244 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8037 (p0) REVERT: B 305 ASP cc_start: 0.6624 (t70) cc_final: 0.6418 (t70) REVERT: B 466 MET cc_start: 0.7031 (tpt) cc_final: 0.6709 (mmm) REVERT: B 553 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5760 (m-10) REVERT: B 580 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6649 (mpp) REVERT: F 27 GLN cc_start: 0.8137 (pm20) cc_final: 0.7696 (pm20) REVERT: I 20 LEU cc_start: 0.8457 (mp) cc_final: 0.8250 (mt) outliers start: 49 outliers final: 19 residues processed: 253 average time/residue: 1.0933 time to fit residues: 313.7272 Evaluate side-chains 238 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR 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 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 ASN A 80 HIS A 196 ASN A 230 GLN A 364 GLN G 86 ASN B 80 HIS B 502 HIS I 86 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17538 Z= 0.352 Angle : 0.618 8.148 23850 Z= 0.316 Chirality : 0.047 0.160 2547 Planarity : 0.005 0.047 3099 Dihedral : 4.893 18.801 2337 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.04 % Allowed : 17.71 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2127 helix: -2.42 (0.38), residues: 135 sheet: -0.63 (0.16), residues: 966 loop : -0.62 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 336 HIS 0.015 0.001 HIS A 80 PHE 0.011 0.001 PHE F 93 TYR 0.019 0.002 TYR A 203 ARG 0.009 0.000 ARG D 24 *********************** 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 280 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 223 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: C 133 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: C 305 ASP cc_start: 0.7086 (t0) cc_final: 0.6607 (t0) REVERT: C 365 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7570 (ptpp) REVERT: C 498 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.5475 (mpt) REVERT: D 91 TYR cc_start: 0.8075 (m-80) cc_final: 0.7703 (m-80) REVERT: H 46 GLU cc_start: 0.7476 (tt0) cc_final: 0.6906 (mt-10) REVERT: A 133 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: A 498 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6166 (mpt) REVERT: E 27 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: G 19 LYS cc_start: 0.8294 (tptt) cc_final: 0.8037 (tptp) REVERT: G 38 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.6913 (ptt180) REVERT: B 133 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: B 244 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8094 (p0) REVERT: B 466 MET cc_start: 0.7099 (tpt) cc_final: 0.6790 (mmm) REVERT: B 580 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6711 (mpp) outliers start: 57 outliers final: 20 residues processed: 256 average time/residue: 1.2250 time to fit residues: 352.5061 Evaluate side-chains 245 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 365 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 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 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 43 LYS 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 368 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 173 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 502 HIS H 86 ASN A 80 HIS A 230 GLN A 364 GLN B 80 HIS B 230 GLN B 502 HIS I 86 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17538 Z= 0.327 Angle : 0.607 8.038 23850 Z= 0.312 Chirality : 0.047 0.200 2547 Planarity : 0.005 0.046 3099 Dihedral : 4.894 18.619 2337 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.09 % Allowed : 18.19 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2127 helix: -2.43 (0.38), residues: 135 sheet: -0.67 (0.16), residues: 957 loop : -0.60 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 336 HIS 0.016 0.001 HIS A 80 PHE 0.011 0.001 PHE F 93 TYR 0.018 0.002 TYR A 203 ARG 0.011 0.001 ARG F 24 *********************** 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 277 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: C 104 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6497 (ptt) REVERT: C 133 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: C 305 ASP cc_start: 0.7099 (t0) cc_final: 0.6631 (t0) REVERT: C 365 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7567 (ptpp) REVERT: C 498 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.5404 (mpt) REVERT: D 91 TYR cc_start: 0.8064 (m-80) cc_final: 0.7768 (m-80) REVERT: D 109 GLU cc_start: 0.5782 (tp30) cc_final: 0.5365 (tp30) REVERT: H 38 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.6683 (ptp-170) REVERT: A 133 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: A 498 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6132 (mpt) REVERT: E 27 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: G 38 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6912 (ptt180) REVERT: B 104 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6447 (ptt) REVERT: B 133 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: B 244 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 456 MET cc_start: 0.0745 (OUTLIER) cc_final: -0.1152 (ppp) REVERT: B 466 MET cc_start: 0.7101 (tpt) cc_final: 0.6787 (mmm) REVERT: B 553 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5872 (m-10) REVERT: B 580 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6713 (mpp) outliers start: 58 outliers final: 24 residues processed: 246 average time/residue: 1.1762 time to fit residues: 326.0947 Evaluate side-chains 253 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 365 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 56 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 H residue 121 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 43 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 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 89 VAL 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 127 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 161 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 315 ASN C 502 HIS H 86 ASN A 80 HIS A 230 GLN A 364 GLN A 502 HIS G 86 ASN B 80 HIS B 475 ASN B 502 HIS I 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17538 Z= 0.243 Angle : 0.577 7.513 23850 Z= 0.294 Chirality : 0.046 0.187 2547 Planarity : 0.005 0.046 3099 Dihedral : 4.681 17.183 2337 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.15 % Allowed : 18.29 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2127 helix: -1.89 (0.43), residues: 117 sheet: -0.61 (0.17), residues: 909 loop : -0.62 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 336 HIS 0.016 0.001 HIS A 80 PHE 0.010 0.001 PHE A 337 TYR 0.019 0.001 TYR A 203 ARG 0.012 0.000 ARG E 24 *********************** 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 282 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 223 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: C 104 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6616 (ptt) REVERT: C 133 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: C 305 ASP cc_start: 0.7112 (t0) cc_final: 0.6606 (t0) REVERT: C 456 MET cc_start: 0.0028 (OUTLIER) cc_final: -0.2292 (ppp) REVERT: C 498 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.5315 (mpt) REVERT: D 91 TYR cc_start: 0.8057 (m-80) cc_final: 0.7733 (m-80) REVERT: D 109 GLU cc_start: 0.5617 (tp30) cc_final: 0.5312 (tp30) REVERT: H 38 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6691 (ptp-170) REVERT: H 92 ASP cc_start: 0.7798 (m-30) cc_final: 0.7414 (m-30) REVERT: A 133 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 498 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6142 (mpt) REVERT: E 27 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: G 38 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6850 (ptt180) REVERT: B 104 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6286 (ptt) REVERT: B 133 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: B 244 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8095 (p0) REVERT: B 456 MET cc_start: 0.0745 (OUTLIER) cc_final: -0.1154 (ppp) REVERT: B 466 MET cc_start: 0.7064 (tpt) cc_final: 0.6763 (mmm) REVERT: B 553 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5799 (m-10) REVERT: B 580 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6584 (mpp) REVERT: I 38 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7778 (ttm170) outliers start: 59 outliers final: 24 residues processed: 249 average time/residue: 1.1592 time to fit residues: 325.4824 Evaluate side-chains 251 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain D residue 56 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 85 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 537 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 56 THR Chi-restraints excluded: chain F residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 172 optimal weight: 0.0870 chunk 180 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 502 HIS H 86 ASN A 80 HIS A 230 GLN A 364 GLN A 502 HIS B 80 HIS B 230 GLN B 502 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17538 Z= 0.246 Angle : 0.579 7.443 23850 Z= 0.296 Chirality : 0.046 0.180 2547 Planarity : 0.005 0.052 3099 Dihedral : 4.675 17.118 2337 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.93 % Allowed : 18.93 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2127 helix: -1.85 (0.44), residues: 117 sheet: -0.61 (0.17), residues: 918 loop : -0.58 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 61 HIS 0.016 0.001 HIS A 80 PHE 0.010 0.001 PHE A 337 TYR 0.018 0.001 TYR A 203 ARG 0.012 0.001 ARG E 24 *********************** 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 272 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 217 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: C 103 ASP cc_start: 0.7591 (p0) cc_final: 0.7374 (p0) REVERT: C 133 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: C 305 ASP cc_start: 0.7106 (t0) cc_final: 0.6608 (t0) REVERT: C 456 MET cc_start: 0.0039 (OUTLIER) cc_final: -0.2275 (ppp) REVERT: D 91 TYR cc_start: 0.8045 (m-80) cc_final: 0.7759 (m-80) REVERT: D 94 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: D 109 GLU cc_start: 0.5587 (tp30) cc_final: 0.5258 (tp30) REVERT: H 38 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6692 (ptp-170) REVERT: H 92 ASP cc_start: 0.7778 (m-30) cc_final: 0.7396 (m-30) REVERT: A 133 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: A 498 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6166 (mpt) REVERT: E 27 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: G 38 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6796 (ptt180) REVERT: B 104 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6290 (ptt) REVERT: B 133 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: B 244 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 456 MET cc_start: 0.0662 (OUTLIER) cc_final: -0.1227 (ppp) REVERT: B 466 MET cc_start: 0.7031 (tpt) cc_final: 0.6735 (mmm) REVERT: B 498 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.5305 (mpt) REVERT: B 580 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6575 (mpp) REVERT: I 38 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7778 (ttm170) outliers start: 55 outliers final: 23 residues processed: 241 average time/residue: 1.1480 time to fit residues: 312.2973 Evaluate side-chains 248 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain D residue 94 GLN 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 H residue 121 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 43 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 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 537 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 F residue 89 VAL Chi-restraints excluded: chain I residue 89 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS C 502 HIS H 86 ASN A 80 HIS A 230 GLN A 364 GLN A 502 HIS G 86 ASN B 80 HIS B 230 GLN B 309 ASN B 502 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17538 Z= 0.223 Angle : 0.567 7.251 23850 Z= 0.290 Chirality : 0.046 0.172 2547 Planarity : 0.005 0.055 3099 Dihedral : 4.584 16.476 2337 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.40 % Allowed : 19.52 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2127 helix: -1.78 (0.44), residues: 117 sheet: -0.62 (0.17), residues: 921 loop : -0.54 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 61 HIS 0.017 0.001 HIS C 80 PHE 0.010 0.001 PHE A 337 TYR 0.019 0.001 TYR A 203 ARG 0.013 0.000 ARG E 24 ********************** 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 267 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 222 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: C 133 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: C 305 ASP cc_start: 0.7058 (t0) cc_final: 0.6574 (t0) REVERT: C 456 MET cc_start: 0.0045 (OUTLIER) cc_final: -0.2276 (ppp) REVERT: D 91 TYR cc_start: 0.8027 (m-80) cc_final: 0.7733 (m-80) REVERT: D 109 GLU cc_start: 0.5463 (tp30) cc_final: 0.5180 (tp30) REVERT: H 38 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.6687 (ptp-170) REVERT: H 92 ASP cc_start: 0.7782 (m-30) cc_final: 0.7407 (m-30) REVERT: A 133 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: A 498 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6159 (mpt) REVERT: E 27 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: G 38 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6760 (ptt180) REVERT: B 104 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6333 (ptt) REVERT: B 133 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: B 244 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 456 MET cc_start: 0.0722 (OUTLIER) cc_final: -0.1137 (ppp) REVERT: B 466 MET cc_start: 0.7018 (tpt) cc_final: 0.6722 (mmm) REVERT: B 498 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.5262 (mpt) REVERT: B 580 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6598 (mpp) outliers start: 45 outliers final: 25 residues processed: 239 average time/residue: 1.2252 time to fit residues: 331.0498 Evaluate side-chains 252 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 553 PHE 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 H residue 121 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 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 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 43 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 368 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 537 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 F residue 89 VAL Chi-restraints excluded: chain I residue 89 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS H 86 ASN A 80 HIS A 230 GLN A 364 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 230 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.167680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123011 restraints weight = 22873.577| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.60 r_work: 0.3411 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 17538 Z= 0.506 Angle : 0.709 9.257 23850 Z= 0.364 Chirality : 0.051 0.178 2547 Planarity : 0.005 0.057 3099 Dihedral : 5.319 22.539 2337 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.45 % Allowed : 19.68 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2127 helix: -2.52 (0.36), residues: 132 sheet: -0.70 (0.16), residues: 918 loop : -0.85 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 61 HIS 0.016 0.002 HIS A 80 PHE 0.013 0.002 PHE F 93 TYR 0.015 0.002 TYR B 561 ARG 0.013 0.001 ARG E 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5989.50 seconds wall clock time: 105 minutes 34.97 seconds (6334.97 seconds total)