Starting phenix.real_space_refine on Sun Jul 27 22:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk0_32554/07_2025/7wk0_32554.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk0_32554/07_2025/7wk0_32554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2025/7wk0_32554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2025/7wk0_32554.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2025/7wk0_32554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2025/7wk0_32554.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 34 5.16 5 C 6154 2.51 5 N 1646 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.54, per 1000 atoms: 0.78 Number of scatterers: 9724 At special positions: 0 Unit cell: (88.312, 155.344, 110.656, 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 34 16.00 O 1890 8.00 N 1646 7.00 C 6154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 25 sheets defined 2.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.804A pdb=" N GLU B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.567A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.798A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.936A pdb=" N GLY A 50 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 60 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 48 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 94 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.873A pdb=" N GLY A 152 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.507A pdb=" N THR A 164 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 209 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 222 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 220 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 213 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 218 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.868A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.747A pdb=" N ILE B 74 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 20 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.503A pdb=" N ILE B 138 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 176 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.752A pdb=" N THR B 147 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 195 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 206 " --> pdb=" O CYS B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.534A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.628A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 48 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR D 60 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY D 50 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.533A pdb=" N LEU D 151 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 193 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 192 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 Processing sheet with id=AB8, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.887A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 47 removed outlier: 5.626A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 47 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.899A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 138 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP E 140 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.674A pdb=" N CYS E 195 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 206 " --> pdb=" O CYS E 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'F' and resid 473 through 474 183 hydrogen bonds defined for protein. 447 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: 3.03 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1593 1.31 - 1.44: 2884 1.44 - 1.56: 5469 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9982 Sorted by residual: bond pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.31e-02 5.83e+03 3.62e+01 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.455 1.397 0.059 1.25e-02 6.40e+03 2.19e+01 bond pdb=" N GLU F 406 " pdb=" CA GLU F 406 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.16e-02 7.43e+03 2.02e+01 bond pdb=" C ILE C 358 " pdb=" O ILE C 358 " ideal model delta sigma weight residual 1.237 1.188 0.050 1.13e-02 7.83e+03 1.93e+01 bond pdb=" CA ASN C 354 " pdb=" C ASN C 354 " ideal model delta sigma weight residual 1.523 1.469 0.053 1.23e-02 6.61e+03 1.89e+01 ... (remaining 9977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13311 1.98 - 3.97: 256 3.97 - 5.95: 38 5.95 - 7.94: 6 7.94 - 9.92: 3 Bond angle restraints: 13614 Sorted by residual: angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 114.31 104.48 9.83 1.29e+00 6.01e-01 5.81e+01 angle pdb=" N VAL F 407 " pdb=" CA VAL F 407 " pdb=" C VAL F 407 " ideal model delta sigma weight residual 111.58 104.58 7.00 1.06e+00 8.90e-01 4.36e+01 angle pdb=" N GLY D 66 " pdb=" CA GLY D 66 " pdb=" C GLY D 66 " ideal model delta sigma weight residual 115.27 107.54 7.73 1.41e+00 5.03e-01 3.00e+01 angle pdb=" N ASN C 448 " pdb=" CA ASN C 448 " pdb=" C ASN C 448 " ideal model delta sigma weight residual 109.24 101.13 8.11 1.67e+00 3.59e-01 2.36e+01 angle pdb=" N SER C 359 " pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 108.74 114.66 -5.92 1.38e+00 5.25e-01 1.84e+01 ... (remaining 13609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5574 17.71 - 35.42: 306 35.42 - 53.14: 45 53.14 - 70.85: 18 70.85 - 88.56: 1 Dihedral angle restraints: 5944 sinusoidal: 2288 harmonic: 3656 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N SER B 192 " pdb=" CA SER B 192 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" N ASN C 448 " pdb=" C ASN C 448 " pdb=" CA ASN C 448 " pdb=" CB ASN C 448 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1322 0.071 - 0.142: 169 0.142 - 0.212: 4 0.212 - 0.283: 2 0.283 - 0.354: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN F 448 " pdb=" N ASN F 448 " pdb=" C ASN F 448 " pdb=" CB ASN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ALA C 372 " pdb=" N ALA C 372 " pdb=" C ALA C 372 " pdb=" CB ALA C 372 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1495 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " 0.257 2.00e-02 2.50e+03 2.18e-01 5.92e+02 pdb=" C7 NAG F 601 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " -0.371 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 400 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C PHE C 400 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE C 400 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL C 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 353 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C TRP C 353 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP C 353 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN C 354 " 0.020 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1603 2.77 - 3.30: 9290 3.30 - 3.83: 15901 3.83 - 4.37: 18585 4.37 - 4.90: 31950 Nonbonded interactions: 77329 Sorted by model distance: nonbonded pdb=" OG SER E 62 " pdb=" OG1 THR E 73 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 71 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP E 91 " pdb=" OG SER E 94 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU E 126 " pdb=" OG1 THR E 133 " model vdw 2.286 3.040 ... (remaining 77324 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 8.670 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.330 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.004 0.079 10000 Z= 0.296 Angle : 0.664 9.922 13652 Z= 0.388 Chirality : 0.045 0.354 1498 Planarity : 0.007 0.218 1764 Dihedral : 11.091 88.559 3568 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.22 % Favored : 87.54 % Rotamer: Outliers : 7.71 % Allowed : 7.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.20), residues: 1252 helix: -5.35 (0.10), residues: 70 sheet: -2.88 (0.22), residues: 452 loop : -3.46 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.002 0.001 HIS B 199 PHE 0.008 0.001 PHE C 375 TYR 0.008 0.001 TYR A 112 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 2) link_NAG-ASN : angle 5.34599 ( 6) hydrogen bonds : bond 0.28683 ( 174) hydrogen bonds : angle 11.39510 ( 447) SS BOND : bond 0.00214 ( 16) SS BOND : angle 0.46490 ( 32) covalent geometry : bond 0.00428 ( 9982) covalent geometry : angle 0.65482 (13614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 237 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.7978 (m) cc_final: 0.7616 (t) REVERT: A 154 LEU cc_start: 0.8591 (tp) cc_final: 0.8217 (tp) REVERT: B 21 THR cc_start: 0.8338 (p) cc_final: 0.8136 (t) REVERT: B 116 SER cc_start: 0.7575 (t) cc_final: 0.7274 (p) REVERT: C 346 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8251 (mtt90) REVERT: C 438 SER cc_start: 0.8294 (m) cc_final: 0.8077 (p) REVERT: C 445 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 448 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7425 (p0) REVERT: C 459 SER cc_start: 0.8501 (p) cc_final: 0.8280 (m) REVERT: C 467 ASP cc_start: 0.7055 (p0) cc_final: 0.6626 (p0) REVERT: C 508 TYR cc_start: 0.8308 (m-80) cc_final: 0.7897 (m-80) REVERT: D 25 SER cc_start: 0.8443 (t) cc_final: 0.8099 (p) REVERT: D 37 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (m) REVERT: D 70 ILE cc_start: 0.8809 (tt) cc_final: 0.8585 (tt) REVERT: D 126 SER cc_start: 0.8376 (m) cc_final: 0.8124 (p) REVERT: D 134 VAL cc_start: 0.8661 (t) cc_final: 0.8455 (m) REVERT: E 78 GLU cc_start: 0.7089 (pm20) cc_final: 0.6506 (pm20) REVERT: E 81 ASP cc_start: 0.8128 (t70) cc_final: 0.7921 (t70) REVERT: E 147 THR cc_start: 0.8027 (m) cc_final: 0.7546 (p) REVERT: F 355 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7100 (mtp85) REVERT: F 362 VAL cc_start: 0.8501 (t) cc_final: 0.8069 (p) REVERT: F 375 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: F 377 PHE cc_start: 0.7852 (t80) cc_final: 0.7636 (t80) REVERT: F 394 ASN cc_start: 0.7326 (m-40) cc_final: 0.6887 (m-40) REVERT: F 439 ASN cc_start: 0.8213 (t0) cc_final: 0.7927 (t0) REVERT: F 503 VAL cc_start: 0.8803 (p) cc_final: 0.8588 (t) REVERT: F 517 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6655 (tm) outliers start: 82 outliers final: 35 residues processed: 296 average time/residue: 0.2398 time to fit residues: 95.9022 Evaluate side-chains 250 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 33 HIS B 88 GLN B 110 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 409 GLN C 437 ASN C 448 ASN C 481 ASN D 3 GLN D 118 GLN E 33 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 110 GLN E 172 ASN F 394 ASN F 409 GLN F 448 ASN F 474 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112967 restraints weight = 14635.431| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.23 r_work: 0.3324 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10000 Z= 0.217 Angle : 0.661 7.238 13652 Z= 0.340 Chirality : 0.046 0.224 1498 Planarity : 0.005 0.052 1764 Dihedral : 8.345 71.990 1517 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 5.73 % Allowed : 13.53 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.18 (0.21), residues: 1252 helix: -4.95 (0.34), residues: 56 sheet: -2.16 (0.25), residues: 396 loop : -3.10 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 436 HIS 0.004 0.001 HIS D 100 PHE 0.026 0.002 PHE C 377 TYR 0.017 0.002 TYR D 95 ARG 0.005 0.001 ARG B 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 2) link_NAG-ASN : angle 3.79305 ( 6) hydrogen bonds : bond 0.04213 ( 174) hydrogen bonds : angle 7.44754 ( 447) SS BOND : bond 0.00458 ( 16) SS BOND : angle 0.95431 ( 32) covalent geometry : bond 0.00486 ( 9982) covalent geometry : angle 0.65537 (13614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8183 (m) cc_final: 0.7885 (p) REVERT: A 25 SER cc_start: 0.8333 (t) cc_final: 0.8087 (m) REVERT: A 55 SER cc_start: 0.8280 (m) cc_final: 0.7890 (t) REVERT: A 154 LEU cc_start: 0.8823 (tp) cc_final: 0.8452 (tp) REVERT: B 14 PRO cc_start: 0.8476 (Cg_endo) cc_final: 0.8197 (Cg_exo) REVERT: B 116 SER cc_start: 0.8278 (t) cc_final: 0.8067 (p) REVERT: B 151 LYS cc_start: 0.7396 (ttmm) cc_final: 0.7120 (ttmm) REVERT: C 346 ARG cc_start: 0.8727 (mtt-85) cc_final: 0.8297 (mtt180) REVERT: C 354 ASN cc_start: 0.8504 (t0) cc_final: 0.8217 (t0) REVERT: C 355 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7755 (ttm170) REVERT: C 360 ASN cc_start: 0.8207 (m110) cc_final: 0.7930 (t0) REVERT: C 481 ASN cc_start: 0.8366 (m-40) cc_final: 0.8138 (m110) REVERT: C 488 CYS cc_start: 0.7228 (m) cc_final: 0.6799 (m) REVERT: C 508 TYR cc_start: 0.8657 (m-80) cc_final: 0.8427 (m-80) REVERT: C 509 ARG cc_start: 0.8873 (mtt-85) cc_final: 0.8546 (mtt180) REVERT: C 518 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8354 (mp) REVERT: D 25 SER cc_start: 0.8767 (t) cc_final: 0.8433 (p) REVERT: D 70 ILE cc_start: 0.8964 (tt) cc_final: 0.8757 (tt) REVERT: D 80 TYR cc_start: 0.8638 (m-80) cc_final: 0.7790 (m-80) REVERT: D 126 SER cc_start: 0.8678 (m) cc_final: 0.8388 (p) REVERT: D 158 TYR cc_start: 0.7789 (p90) cc_final: 0.7532 (p90) REVERT: E 51 SER cc_start: 0.8093 (m) cc_final: 0.7725 (p) REVERT: E 77 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7419 (m) REVERT: E 78 GLU cc_start: 0.7866 (pm20) cc_final: 0.7482 (pm20) REVERT: E 81 ASP cc_start: 0.8434 (t70) cc_final: 0.8054 (t70) REVERT: E 119 LEU cc_start: 0.6859 (mm) cc_final: 0.6584 (tp) REVERT: E 198 THR cc_start: 0.7981 (m) cc_final: 0.7707 (p) REVERT: F 362 VAL cc_start: 0.8584 (t) cc_final: 0.8230 (p) REVERT: F 386 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8110 (mmtt) REVERT: F 394 ASN cc_start: 0.8020 (m110) cc_final: 0.7705 (m110) REVERT: F 439 ASN cc_start: 0.8502 (t0) cc_final: 0.8181 (t0) REVERT: F 503 VAL cc_start: 0.8916 (p) cc_final: 0.8699 (t) outliers start: 61 outliers final: 40 residues processed: 265 average time/residue: 0.2853 time to fit residues: 103.8410 Evaluate side-chains 246 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 48 optimal weight: 0.0030 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 168 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN F 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107618 restraints weight = 15071.925| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.67 r_work: 0.3229 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10000 Z= 0.212 Angle : 0.651 7.311 13652 Z= 0.332 Chirality : 0.045 0.207 1498 Planarity : 0.005 0.045 1764 Dihedral : 7.873 73.462 1488 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 6.02 % Allowed : 15.51 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.80 (0.22), residues: 1252 helix: -5.00 (0.27), residues: 56 sheet: -1.93 (0.24), residues: 438 loop : -2.80 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.014 0.001 HIS B 190 PHE 0.025 0.002 PHE C 377 TYR 0.015 0.002 TYR D 95 ARG 0.006 0.001 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 3.47232 ( 6) hydrogen bonds : bond 0.04100 ( 174) hydrogen bonds : angle 6.96956 ( 447) SS BOND : bond 0.00444 ( 16) SS BOND : angle 1.00943 ( 32) covalent geometry : bond 0.00480 ( 9982) covalent geometry : angle 0.64620 (13614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8036 (m) cc_final: 0.7804 (p) REVERT: A 55 SER cc_start: 0.8298 (m) cc_final: 0.7822 (t) REVERT: A 85 SER cc_start: 0.8355 (t) cc_final: 0.7949 (t) REVERT: A 154 LEU cc_start: 0.8724 (tp) cc_final: 0.8312 (tp) REVERT: B 6 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: B 14 PRO cc_start: 0.8493 (Cg_endo) cc_final: 0.8244 (Cg_exo) REVERT: B 55 SER cc_start: 0.7990 (t) cc_final: 0.7623 (m) REVERT: B 76 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7754 (mpp80) REVERT: C 346 ARG cc_start: 0.8626 (mtt-85) cc_final: 0.8110 (mtt180) REVERT: C 354 ASN cc_start: 0.8301 (t0) cc_final: 0.8049 (t0) REVERT: C 355 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7641 (ttm170) REVERT: C 360 ASN cc_start: 0.8225 (m110) cc_final: 0.7861 (t0) REVERT: C 467 ASP cc_start: 0.7255 (p0) cc_final: 0.6837 (p0) REVERT: C 481 ASN cc_start: 0.8471 (m-40) cc_final: 0.7869 (t0) REVERT: C 508 TYR cc_start: 0.8524 (m-80) cc_final: 0.8209 (m-80) REVERT: C 509 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8543 (mtt180) REVERT: C 511 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8390 (t) REVERT: C 518 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8269 (mp) REVERT: D 25 SER cc_start: 0.8664 (t) cc_final: 0.8239 (p) REVERT: D 60 TYR cc_start: 0.8353 (m-80) cc_final: 0.8105 (m-80) REVERT: D 79 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (tp) REVERT: D 80 TYR cc_start: 0.8444 (m-80) cc_final: 0.8202 (m-80) REVERT: D 126 SER cc_start: 0.8647 (m) cc_final: 0.8351 (p) REVERT: D 158 TYR cc_start: 0.7964 (p90) cc_final: 0.7575 (p90) REVERT: E 51 SER cc_start: 0.8145 (m) cc_final: 0.7778 (p) REVERT: E 75 SER cc_start: 0.8329 (t) cc_final: 0.8110 (t) REVERT: E 77 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7067 (t) REVERT: E 78 GLU cc_start: 0.7820 (pm20) cc_final: 0.7517 (pm20) REVERT: E 81 ASP cc_start: 0.8305 (t70) cc_final: 0.7968 (t70) REVERT: F 354 ASN cc_start: 0.7808 (t0) cc_final: 0.7331 (t0) REVERT: F 362 VAL cc_start: 0.8374 (t) cc_final: 0.8007 (p) REVERT: F 386 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8035 (mmtt) outliers start: 64 outliers final: 37 residues processed: 255 average time/residue: 0.2457 time to fit residues: 86.0545 Evaluate side-chains 254 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.0020 chunk 81 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 90 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 110 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 394 ASN D 74 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN F 450 ASN F 481 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109487 restraints weight = 14565.147| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.36 r_work: 0.3221 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10000 Z= 0.211 Angle : 0.656 10.951 13652 Z= 0.334 Chirality : 0.045 0.213 1498 Planarity : 0.005 0.047 1764 Dihedral : 7.825 75.094 1485 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 6.11 % Allowed : 16.54 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.57 (0.22), residues: 1252 helix: -5.00 (0.24), residues: 56 sheet: -1.64 (0.26), residues: 406 loop : -2.70 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.002 PHE C 375 TYR 0.015 0.002 TYR A 189 ARG 0.004 0.001 ARG F 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 2) link_NAG-ASN : angle 3.45479 ( 6) hydrogen bonds : bond 0.03853 ( 174) hydrogen bonds : angle 6.58155 ( 447) SS BOND : bond 0.00438 ( 16) SS BOND : angle 1.01099 ( 32) covalent geometry : bond 0.00480 ( 9982) covalent geometry : angle 0.65129 (13614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8576 (m) cc_final: 0.8342 (p) REVERT: A 17 SER cc_start: 0.8105 (m) cc_final: 0.7867 (p) REVERT: A 32 TYR cc_start: 0.8801 (m-80) cc_final: 0.8483 (m-80) REVERT: A 55 SER cc_start: 0.8405 (m) cc_final: 0.7893 (t) REVERT: A 85 SER cc_start: 0.8428 (t) cc_final: 0.8037 (t) REVERT: A 154 LEU cc_start: 0.8793 (tp) cc_final: 0.8390 (tp) REVERT: B 6 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: B 55 SER cc_start: 0.8129 (t) cc_final: 0.7755 (m) REVERT: B 76 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7940 (mpp80) REVERT: B 151 LYS cc_start: 0.7349 (ttmm) cc_final: 0.7032 (ttmm) REVERT: B 200 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5328 (pm20) REVERT: C 346 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8198 (mtt180) REVERT: C 354 ASN cc_start: 0.8464 (t0) cc_final: 0.8183 (t0) REVERT: C 355 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7775 (ttm170) REVERT: C 360 ASN cc_start: 0.8356 (m110) cc_final: 0.7972 (t0) REVERT: C 467 ASP cc_start: 0.7375 (p0) cc_final: 0.6892 (p0) REVERT: C 481 ASN cc_start: 0.8563 (m-40) cc_final: 0.8081 (t0) REVERT: C 493 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.8259 (mmt90) REVERT: C 511 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8476 (t) REVERT: C 518 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (mp) REVERT: D 25 SER cc_start: 0.8760 (t) cc_final: 0.8371 (p) REVERT: D 60 TYR cc_start: 0.8447 (m-80) cc_final: 0.8090 (m-80) REVERT: D 80 TYR cc_start: 0.8530 (m-80) cc_final: 0.8300 (m-80) REVERT: D 100 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.6068 (m90) REVERT: D 126 SER cc_start: 0.8730 (m) cc_final: 0.8436 (p) REVERT: D 158 TYR cc_start: 0.8015 (p90) cc_final: 0.7619 (p90) REVERT: E 51 SER cc_start: 0.8225 (m) cc_final: 0.7870 (p) REVERT: E 75 SER cc_start: 0.8361 (t) cc_final: 0.8156 (t) REVERT: E 81 ASP cc_start: 0.8361 (t70) cc_final: 0.7985 (t0) REVERT: E 147 THR cc_start: 0.8192 (m) cc_final: 0.7696 (p) REVERT: F 354 ASN cc_start: 0.7860 (t0) cc_final: 0.7530 (t0) REVERT: F 362 VAL cc_start: 0.8460 (t) cc_final: 0.8093 (p) REVERT: F 386 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8095 (mmtt) REVERT: F 422 ASN cc_start: 0.8800 (m-40) cc_final: 0.8536 (m-40) outliers start: 65 outliers final: 41 residues processed: 255 average time/residue: 0.2175 time to fit residues: 76.6750 Evaluate side-chains 248 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 88 optimal weight: 0.0030 chunk 113 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 80 optimal weight: 0.0870 chunk 96 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 6 optimal weight: 0.0770 overall best weight: 0.1526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN F 450 ASN F 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111951 restraints weight = 14572.888| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.38 r_work: 0.3290 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10000 Z= 0.118 Angle : 0.596 8.494 13652 Z= 0.304 Chirality : 0.044 0.191 1498 Planarity : 0.005 0.056 1764 Dihedral : 7.508 76.338 1485 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 4.98 % Allowed : 18.23 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.34 (0.22), residues: 1252 helix: -4.99 (0.22), residues: 56 sheet: -1.46 (0.27), residues: 398 loop : -2.53 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.003 0.001 HIS D 99 PHE 0.019 0.001 PHE C 377 TYR 0.010 0.001 TYR D 95 ARG 0.004 0.000 ARG F 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 2.64625 ( 6) hydrogen bonds : bond 0.03386 ( 174) hydrogen bonds : angle 6.13348 ( 447) SS BOND : bond 0.00332 ( 16) SS BOND : angle 1.03364 ( 32) covalent geometry : bond 0.00271 ( 9982) covalent geometry : angle 0.59203 (13614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8024 (m) cc_final: 0.7815 (p) REVERT: A 55 SER cc_start: 0.8226 (m) cc_final: 0.7727 (t) REVERT: A 85 SER cc_start: 0.8414 (t) cc_final: 0.8058 (t) REVERT: A 154 LEU cc_start: 0.8735 (tp) cc_final: 0.8332 (tp) REVERT: B 6 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: B 76 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7964 (mpp80) REVERT: B 151 LYS cc_start: 0.7182 (ttmm) cc_final: 0.6957 (ttmm) REVERT: B 200 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.5428 (pm20) REVERT: C 346 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8157 (mtt180) REVERT: C 354 ASN cc_start: 0.8498 (t0) cc_final: 0.8272 (t0) REVERT: C 355 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7827 (ttm170) REVERT: C 357 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7765 (mtp-110) REVERT: C 360 ASN cc_start: 0.8314 (m110) cc_final: 0.7977 (t0) REVERT: C 448 ASN cc_start: 0.7864 (p0) cc_final: 0.7511 (p0) REVERT: C 467 ASP cc_start: 0.7424 (p0) cc_final: 0.6797 (p0) REVERT: C 481 ASN cc_start: 0.8530 (m-40) cc_final: 0.8000 (t0) REVERT: C 489 TYR cc_start: 0.8523 (m-80) cc_final: 0.8113 (m-80) REVERT: C 490 PHE cc_start: 0.8112 (t80) cc_final: 0.7860 (t80) REVERT: C 511 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (t) REVERT: D 25 SER cc_start: 0.8733 (t) cc_final: 0.8360 (p) REVERT: D 74 ASN cc_start: 0.8839 (m-40) cc_final: 0.8625 (m-40) REVERT: D 126 SER cc_start: 0.8699 (m) cc_final: 0.8393 (p) REVERT: E 5 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8498 (p) REVERT: E 51 SER cc_start: 0.8040 (m) cc_final: 0.7633 (p) REVERT: E 81 ASP cc_start: 0.8238 (t70) cc_final: 0.7956 (t0) REVERT: E 147 THR cc_start: 0.8264 (m) cc_final: 0.7767 (p) REVERT: E 198 THR cc_start: 0.7778 (m) cc_final: 0.7482 (p) REVERT: F 354 ASN cc_start: 0.7975 (t0) cc_final: 0.7490 (t0) REVERT: F 362 VAL cc_start: 0.8487 (t) cc_final: 0.8145 (p) REVERT: F 386 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8168 (mmtt) REVERT: F 438 SER cc_start: 0.8667 (m) cc_final: 0.8245 (p) REVERT: F 496 SER cc_start: 0.7852 (t) cc_final: 0.7492 (t) REVERT: F 517 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7193 (tm) outliers start: 53 outliers final: 36 residues processed: 238 average time/residue: 0.2495 time to fit residues: 81.4813 Evaluate side-chains 239 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 37 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 505 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109118 restraints weight = 14655.129| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.38 r_work: 0.3203 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10000 Z= 0.244 Angle : 0.675 9.422 13652 Z= 0.345 Chirality : 0.046 0.215 1498 Planarity : 0.005 0.050 1764 Dihedral : 7.707 76.944 1481 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 5.55 % Allowed : 18.52 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.26 (0.23), residues: 1252 helix: -4.99 (0.23), residues: 56 sheet: -1.45 (0.26), residues: 424 loop : -2.45 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 436 HIS 0.005 0.001 HIS A 213 PHE 0.016 0.002 PHE C 375 TYR 0.016 0.002 TYR D 95 ARG 0.004 0.000 ARG F 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 2) link_NAG-ASN : angle 2.99650 ( 6) hydrogen bonds : bond 0.03905 ( 174) hydrogen bonds : angle 6.24776 ( 447) SS BOND : bond 0.00453 ( 16) SS BOND : angle 1.12110 ( 32) covalent geometry : bond 0.00556 ( 9982) covalent geometry : angle 0.67103 (13614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8394 (t) cc_final: 0.8097 (m) REVERT: A 55 SER cc_start: 0.8379 (m) cc_final: 0.7868 (t) REVERT: A 85 SER cc_start: 0.8350 (t) cc_final: 0.7946 (t) REVERT: A 154 LEU cc_start: 0.8784 (tp) cc_final: 0.8384 (tp) REVERT: A 188 LEU cc_start: 0.8025 (mm) cc_final: 0.7704 (mt) REVERT: B 6 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: B 55 SER cc_start: 0.8147 (t) cc_final: 0.7781 (m) REVERT: B 76 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7979 (mpp80) REVERT: C 346 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8251 (mtt180) REVERT: C 354 ASN cc_start: 0.8434 (t0) cc_final: 0.8201 (t0) REVERT: C 355 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7801 (ttm170) REVERT: C 360 ASN cc_start: 0.8328 (m110) cc_final: 0.7943 (t0) REVERT: C 438 SER cc_start: 0.8501 (m) cc_final: 0.8255 (p) REVERT: C 448 ASN cc_start: 0.7997 (p0) cc_final: 0.7628 (p0) REVERT: C 454 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7961 (ttm-80) REVERT: C 467 ASP cc_start: 0.7364 (p0) cc_final: 0.6602 (p0) REVERT: C 481 ASN cc_start: 0.8506 (m-40) cc_final: 0.8211 (t0) REVERT: C 511 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8490 (t) REVERT: D 25 SER cc_start: 0.8767 (t) cc_final: 0.8378 (p) REVERT: D 100 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6063 (m90) REVERT: D 101 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: D 126 SER cc_start: 0.8765 (m) cc_final: 0.8470 (p) REVERT: D 133 SER cc_start: 0.8503 (t) cc_final: 0.8140 (t) REVERT: E 5 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8471 (p) REVERT: E 51 SER cc_start: 0.8254 (m) cc_final: 0.7882 (p) REVERT: E 81 ASP cc_start: 0.8310 (t70) cc_final: 0.7947 (t0) REVERT: E 147 THR cc_start: 0.8229 (m) cc_final: 0.7718 (p) REVERT: E 150 TRP cc_start: 0.8167 (m100) cc_final: 0.7896 (m100) REVERT: E 198 THR cc_start: 0.7875 (m) cc_final: 0.7522 (p) REVERT: F 362 VAL cc_start: 0.8433 (t) cc_final: 0.8059 (p) REVERT: F 375 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: F 386 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8170 (mmtt) REVERT: F 438 SER cc_start: 0.8619 (m) cc_final: 0.8201 (p) REVERT: F 496 SER cc_start: 0.8052 (t) cc_final: 0.7751 (t) outliers start: 59 outliers final: 41 residues processed: 245 average time/residue: 0.2476 time to fit residues: 84.7855 Evaluate side-chains 259 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.0020 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 chunk 26 optimal weight: 0.5980 chunk 113 optimal weight: 0.4980 chunk 103 optimal weight: 0.0970 chunk 45 optimal weight: 0.4980 chunk 55 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 0.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E 6 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 505 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111546 restraints weight = 14748.584| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.39 r_work: 0.3263 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10000 Z= 0.118 Angle : 0.604 8.292 13652 Z= 0.307 Chirality : 0.044 0.202 1498 Planarity : 0.005 0.048 1764 Dihedral : 7.402 77.141 1481 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.98 % Allowed : 19.64 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.13 (0.23), residues: 1252 helix: -4.94 (0.23), residues: 56 sheet: -1.42 (0.26), residues: 428 loop : -2.33 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.003 0.001 HIS D 99 PHE 0.021 0.001 PHE C 377 TYR 0.012 0.001 TYR C 508 ARG 0.003 0.000 ARG B 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 2) link_NAG-ASN : angle 2.57852 ( 6) hydrogen bonds : bond 0.03338 ( 174) hydrogen bonds : angle 5.90957 ( 447) SS BOND : bond 0.00321 ( 16) SS BOND : angle 0.81782 ( 32) covalent geometry : bond 0.00274 ( 9982) covalent geometry : angle 0.60075 (13614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.8231 (m) cc_final: 0.7677 (t) REVERT: A 85 SER cc_start: 0.8320 (t) cc_final: 0.7966 (t) REVERT: A 154 LEU cc_start: 0.8745 (tp) cc_final: 0.8332 (tp) REVERT: B 6 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: B 46 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7944 (m) REVERT: B 76 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7958 (mpp80) REVERT: B 151 LYS cc_start: 0.7217 (ttmm) cc_final: 0.7013 (ttmm) REVERT: B 173 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6869 (mmmm) REVERT: B 200 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: C 346 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.8180 (mtt180) REVERT: C 425 LEU cc_start: 0.8287 (mp) cc_final: 0.8057 (mt) REVERT: C 448 ASN cc_start: 0.7900 (p0) cc_final: 0.7519 (p0) REVERT: C 454 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7935 (ttm-80) REVERT: C 467 ASP cc_start: 0.7397 (p0) cc_final: 0.6608 (p0) REVERT: C 481 ASN cc_start: 0.8480 (m-40) cc_final: 0.8173 (t160) REVERT: C 489 TYR cc_start: 0.8431 (m-80) cc_final: 0.8006 (m-80) REVERT: C 511 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8477 (t) REVERT: D 25 SER cc_start: 0.8724 (t) cc_final: 0.8360 (p) REVERT: D 100 HIS cc_start: 0.6309 (OUTLIER) cc_final: 0.5981 (m90) REVERT: D 126 SER cc_start: 0.8710 (m) cc_final: 0.8386 (p) REVERT: D 133 SER cc_start: 0.8545 (t) cc_final: 0.8215 (t) REVERT: D 172 LEU cc_start: 0.6897 (tp) cc_final: 0.6542 (mt) REVERT: E 5 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8515 (p) REVERT: E 51 SER cc_start: 0.8030 (m) cc_final: 0.7696 (p) REVERT: E 81 ASP cc_start: 0.8171 (t70) cc_final: 0.7927 (t0) REVERT: E 147 THR cc_start: 0.8256 (m) cc_final: 0.7775 (p) REVERT: E 150 TRP cc_start: 0.8067 (m100) cc_final: 0.7861 (m100) REVERT: E 198 THR cc_start: 0.7595 (m) cc_final: 0.7320 (p) REVERT: F 362 VAL cc_start: 0.8464 (t) cc_final: 0.8133 (p) REVERT: F 386 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8186 (mmtt) REVERT: F 438 SER cc_start: 0.8676 (m) cc_final: 0.8261 (p) REVERT: F 517 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7149 (tm) outliers start: 53 outliers final: 38 residues processed: 244 average time/residue: 0.2439 time to fit residues: 81.2055 Evaluate side-chains 244 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 108 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 122 optimal weight: 0.0040 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110111 restraints weight = 14828.403| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.39 r_work: 0.3237 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10000 Z= 0.169 Angle : 0.632 8.947 13652 Z= 0.322 Chirality : 0.045 0.229 1498 Planarity : 0.005 0.045 1764 Dihedral : 7.316 77.618 1479 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 4.98 % Allowed : 20.21 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.99 (0.23), residues: 1252 helix: -5.03 (0.26), residues: 44 sheet: -1.37 (0.26), residues: 428 loop : -2.25 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 436 HIS 0.003 0.001 HIS D 99 PHE 0.014 0.001 PHE C 375 TYR 0.014 0.001 TYR C 508 ARG 0.003 0.000 ARG F 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 2) link_NAG-ASN : angle 2.69651 ( 6) hydrogen bonds : bond 0.03434 ( 174) hydrogen bonds : angle 5.95204 ( 447) SS BOND : bond 0.00362 ( 16) SS BOND : angle 0.97662 ( 32) covalent geometry : bond 0.00389 ( 9982) covalent geometry : angle 0.62887 (13614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8386 (t) cc_final: 0.8162 (m) REVERT: A 32 TYR cc_start: 0.8727 (m-80) cc_final: 0.8428 (m-80) REVERT: A 49 SER cc_start: 0.8695 (t) cc_final: 0.8064 (m) REVERT: A 55 SER cc_start: 0.8258 (m) cc_final: 0.7753 (t) REVERT: A 85 SER cc_start: 0.8322 (t) cc_final: 0.7963 (t) REVERT: A 154 LEU cc_start: 0.8760 (tp) cc_final: 0.8371 (tp) REVERT: B 6 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: B 76 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7879 (mpp80) REVERT: C 346 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8166 (mtt180) REVERT: C 354 ASN cc_start: 0.8419 (t0) cc_final: 0.8215 (t0) REVERT: C 360 ASN cc_start: 0.8354 (m110) cc_final: 0.7984 (t0) REVERT: C 425 LEU cc_start: 0.8322 (mp) cc_final: 0.8058 (mt) REVERT: C 448 ASN cc_start: 0.7931 (p0) cc_final: 0.7535 (p0) REVERT: C 481 ASN cc_start: 0.8467 (m-40) cc_final: 0.8236 (t0) REVERT: C 511 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8485 (t) REVERT: D 25 SER cc_start: 0.8742 (t) cc_final: 0.8376 (p) REVERT: D 100 HIS cc_start: 0.6363 (OUTLIER) cc_final: 0.5934 (m90) REVERT: D 101 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6095 (mp10) REVERT: D 126 SER cc_start: 0.8744 (m) cc_final: 0.8420 (p) REVERT: D 133 SER cc_start: 0.8596 (t) cc_final: 0.8227 (t) REVERT: D 172 LEU cc_start: 0.7150 (tp) cc_final: 0.6817 (mt) REVERT: E 5 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8477 (p) REVERT: E 51 SER cc_start: 0.8098 (m) cc_final: 0.7759 (p) REVERT: E 81 ASP cc_start: 0.8217 (t70) cc_final: 0.7992 (t0) REVERT: E 147 THR cc_start: 0.8263 (m) cc_final: 0.7799 (p) REVERT: E 198 THR cc_start: 0.7668 (m) cc_final: 0.7401 (p) REVERT: F 362 VAL cc_start: 0.8474 (t) cc_final: 0.8137 (p) REVERT: F 386 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8250 (mmtt) REVERT: F 438 SER cc_start: 0.8632 (m) cc_final: 0.8231 (p) outliers start: 53 outliers final: 42 residues processed: 229 average time/residue: 0.3072 time to fit residues: 97.0676 Evaluate side-chains 246 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN D 74 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109020 restraints weight = 14772.677| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.38 r_work: 0.3214 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10000 Z= 0.199 Angle : 0.662 9.498 13652 Z= 0.337 Chirality : 0.046 0.232 1498 Planarity : 0.005 0.061 1764 Dihedral : 7.475 77.778 1479 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 5.45 % Allowed : 20.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.95 (0.23), residues: 1252 helix: -5.02 (0.27), residues: 44 sheet: -1.23 (0.27), residues: 406 loop : -2.28 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 436 HIS 0.003 0.001 HIS D 99 PHE 0.017 0.002 PHE C 429 TYR 0.015 0.002 TYR C 508 ARG 0.012 0.001 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 2) link_NAG-ASN : angle 2.77905 ( 6) hydrogen bonds : bond 0.03576 ( 174) hydrogen bonds : angle 6.03659 ( 447) SS BOND : bond 0.00381 ( 16) SS BOND : angle 1.04767 ( 32) covalent geometry : bond 0.00457 ( 9982) covalent geometry : angle 0.65805 (13614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8361 (t) cc_final: 0.8101 (m) REVERT: A 32 TYR cc_start: 0.8743 (m-80) cc_final: 0.8446 (m-80) REVERT: A 49 SER cc_start: 0.8692 (t) cc_final: 0.8059 (m) REVERT: A 55 SER cc_start: 0.8322 (m) cc_final: 0.7784 (t) REVERT: A 85 SER cc_start: 0.8235 (t) cc_final: 0.7857 (t) REVERT: A 154 LEU cc_start: 0.8770 (tp) cc_final: 0.8356 (tp) REVERT: B 6 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: B 55 SER cc_start: 0.8406 (t) cc_final: 0.8009 (m) REVERT: B 76 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7847 (mpp80) REVERT: C 346 ARG cc_start: 0.8645 (mtt-85) cc_final: 0.8186 (mtt180) REVERT: C 350 VAL cc_start: 0.8492 (t) cc_final: 0.8176 (p) REVERT: C 354 ASN cc_start: 0.8453 (t0) cc_final: 0.8201 (t0) REVERT: C 360 ASN cc_start: 0.8327 (m110) cc_final: 0.7947 (t0) REVERT: C 438 SER cc_start: 0.8495 (m) cc_final: 0.8258 (p) REVERT: C 448 ASN cc_start: 0.7965 (p0) cc_final: 0.7551 (p0) REVERT: C 467 ASP cc_start: 0.7354 (p0) cc_final: 0.6834 (p0) REVERT: C 481 ASN cc_start: 0.8466 (m-40) cc_final: 0.8185 (t0) REVERT: C 511 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8483 (t) REVERT: D 25 SER cc_start: 0.8731 (t) cc_final: 0.8348 (p) REVERT: D 100 HIS cc_start: 0.6503 (OUTLIER) cc_final: 0.6016 (m90) REVERT: D 101 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: D 126 SER cc_start: 0.8766 (m) cc_final: 0.8460 (p) REVERT: D 133 SER cc_start: 0.8522 (t) cc_final: 0.8148 (t) REVERT: E 5 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8408 (p) REVERT: E 51 SER cc_start: 0.8226 (m) cc_final: 0.7913 (p) REVERT: E 81 ASP cc_start: 0.8320 (t70) cc_final: 0.8114 (t0) REVERT: E 147 THR cc_start: 0.8236 (m) cc_final: 0.7769 (p) REVERT: E 198 THR cc_start: 0.7665 (m) cc_final: 0.7410 (p) REVERT: F 362 VAL cc_start: 0.8437 (t) cc_final: 0.8067 (p) REVERT: F 375 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: F 386 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8207 (mmtt) REVERT: F 438 SER cc_start: 0.8642 (m) cc_final: 0.8239 (p) outliers start: 58 outliers final: 46 residues processed: 242 average time/residue: 0.3008 time to fit residues: 102.3285 Evaluate side-chains 259 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 53 optimal weight: 0.0270 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 94 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110796 restraints weight = 14778.560| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.39 r_work: 0.3260 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10000 Z= 0.135 Angle : 0.625 8.723 13652 Z= 0.316 Chirality : 0.044 0.219 1498 Planarity : 0.005 0.053 1764 Dihedral : 7.277 77.820 1479 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 4.51 % Allowed : 20.68 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.87 (0.23), residues: 1252 helix: -5.04 (0.24), residues: 44 sheet: -1.20 (0.27), residues: 410 loop : -2.20 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE C 375 TYR 0.014 0.001 TYR C 508 ARG 0.011 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 2) link_NAG-ASN : angle 2.48462 ( 6) hydrogen bonds : bond 0.03248 ( 174) hydrogen bonds : angle 5.83073 ( 447) SS BOND : bond 0.00303 ( 16) SS BOND : angle 0.86277 ( 32) covalent geometry : bond 0.00313 ( 9982) covalent geometry : angle 0.62215 (13614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8317 (t) cc_final: 0.8093 (m) REVERT: A 32 TYR cc_start: 0.8733 (m-80) cc_final: 0.8419 (m-80) REVERT: A 49 SER cc_start: 0.8678 (t) cc_final: 0.8058 (m) REVERT: A 55 SER cc_start: 0.8197 (m) cc_final: 0.7659 (t) REVERT: A 85 SER cc_start: 0.8325 (t) cc_final: 0.7978 (t) REVERT: A 154 LEU cc_start: 0.8760 (tp) cc_final: 0.8353 (tp) REVERT: B 6 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: B 76 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7793 (mpp80) REVERT: C 346 ARG cc_start: 0.8638 (mtt-85) cc_final: 0.8156 (mtt180) REVERT: C 354 ASN cc_start: 0.8431 (t0) cc_final: 0.8228 (t0) REVERT: C 360 ASN cc_start: 0.8303 (m110) cc_final: 0.7956 (t0) REVERT: C 448 ASN cc_start: 0.7920 (p0) cc_final: 0.7546 (p0) REVERT: C 467 ASP cc_start: 0.7316 (p0) cc_final: 0.6869 (p0) REVERT: C 481 ASN cc_start: 0.8447 (m-40) cc_final: 0.8204 (t0) REVERT: C 486 PHE cc_start: 0.8686 (m-10) cc_final: 0.8317 (m-80) REVERT: C 494 SER cc_start: 0.8315 (m) cc_final: 0.8090 (p) REVERT: C 511 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8488 (t) REVERT: D 25 SER cc_start: 0.8711 (t) cc_final: 0.8360 (p) REVERT: D 100 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5917 (m90) REVERT: D 101 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6155 (mp10) REVERT: D 126 SER cc_start: 0.8746 (m) cc_final: 0.8423 (p) REVERT: D 133 SER cc_start: 0.8594 (t) cc_final: 0.8226 (t) REVERT: D 178 THR cc_start: 0.8865 (m) cc_final: 0.8425 (p) REVERT: E 51 SER cc_start: 0.8127 (m) cc_final: 0.7822 (p) REVERT: E 81 ASP cc_start: 0.8313 (t70) cc_final: 0.8095 (t0) REVERT: E 147 THR cc_start: 0.8285 (m) cc_final: 0.7843 (p) REVERT: E 198 THR cc_start: 0.7680 (m) cc_final: 0.7416 (p) REVERT: F 362 VAL cc_start: 0.8484 (t) cc_final: 0.8151 (p) REVERT: F 386 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8257 (mmtt) REVERT: F 438 SER cc_start: 0.8632 (m) cc_final: 0.8280 (p) REVERT: F 517 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7195 (tm) outliers start: 48 outliers final: 41 residues processed: 230 average time/residue: 0.2424 time to fit residues: 77.3014 Evaluate side-chains 247 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.0980 chunk 72 optimal weight: 0.3980 chunk 51 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 37 optimal weight: 0.0040 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.0060 chunk 52 optimal weight: 0.7980 overall best weight: 0.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112515 restraints weight = 14654.961| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.43 r_work: 0.3281 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10000 Z= 0.109 Angle : 0.603 8.109 13652 Z= 0.305 Chirality : 0.044 0.233 1498 Planarity : 0.005 0.051 1764 Dihedral : 7.061 78.199 1479 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 4.89 % Allowed : 20.77 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.68 (0.23), residues: 1252 helix: -5.03 (0.23), residues: 44 sheet: -1.07 (0.27), residues: 414 loop : -2.06 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 167 HIS 0.002 0.001 HIS A 35 PHE 0.030 0.001 PHE C 377 TYR 0.011 0.001 TYR B 179 ARG 0.010 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 2) link_NAG-ASN : angle 2.30357 ( 6) hydrogen bonds : bond 0.03058 ( 174) hydrogen bonds : angle 5.61708 ( 447) SS BOND : bond 0.00278 ( 16) SS BOND : angle 0.74055 ( 32) covalent geometry : bond 0.00254 ( 9982) covalent geometry : angle 0.60123 (13614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5755.52 seconds wall clock time: 103 minutes 58.72 seconds (6238.72 seconds total)