Starting phenix.real_space_refine on Sun Apr 5 15:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u69_63900/04_2026/9u69_63900_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u69_63900/04_2026/9u69_63900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u69_63900/04_2026/9u69_63900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u69_63900/04_2026/9u69_63900.map" model { file = "/net/cci-nas-00/data/ceres_data/9u69_63900/04_2026/9u69_63900_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u69_63900/04_2026/9u69_63900_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 54 5.16 5 C 7111 2.51 5 N 1963 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11306 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 155} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "D" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1250 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "E" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "F" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1250 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "E" 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: 2.75, per 1000 atoms: 0.24 Number of scatterers: 11306 At special positions: 0 Unit cell: (89.38, 83.64, 141.04, 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 54 16.00 O 2178 8.00 N 1963 7.00 C 7111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.02 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 E 401 " - " ASN E 11 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 488.2 milliseconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 35 sheets defined 25.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.510A pdb=" N ASP A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU A 69 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 70 " --> pdb=" O CYS A 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'B' and resid 38 through 58 removed outlier: 3.530A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 123 removed outlier: 3.822A pdb=" N LYS B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.685A pdb=" N ASP C 68 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU C 69 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 70 " --> pdb=" O CYS C 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR C 72 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.514A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 64 through 73 removed outlier: 3.541A pdb=" N ASP E 68 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU E 69 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR E 72 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 184 through 192 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.546A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.621A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.849A pdb=" N GLY B 23 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 40 through 44 removed outlier: 7.855A pdb=" N LEU A 41 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR A 277 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER A 43 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.784A pdb=" N LEU A 50 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 79 " --> pdb=" O MET A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.693A pdb=" N LYS A 258 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 113 through 114 removed outlier: 8.049A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AB1, first strand: chain 'A' and resid 133 through 138 removed outlier: 7.771A pdb=" N SER A 135 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N ALA A 141 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AB3, first strand: chain 'A' and resid 285 through 286 removed outlier: 3.936A pdb=" N CYS A 279 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 64 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 34 removed outlier: 3.612A pdb=" N GLY D 23 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AB6, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB8, first strand: chain 'C' and resid 40 through 44 removed outlier: 7.721A pdb=" N LEU C 41 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N THR C 277 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER C 43 " --> pdb=" O THR C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.750A pdb=" N LEU C 50 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 79 " --> pdb=" O MET C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.633A pdb=" N LYS C 258 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 113 through 115 removed outlier: 6.557A pdb=" N HIS C 253 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE C 176 " --> pdb=" O HIS C 253 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE C 176 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 113 through 115 removed outlier: 6.557A pdb=" N HIS C 253 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE C 176 " --> pdb=" O HIS C 253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 133 through 138 removed outlier: 7.834A pdb=" N SER C 135 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N ALA C 141 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 166 Processing sheet with id=AC6, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.598A pdb=" N ILE C 300 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 32 through 33 removed outlier: 3.523A pdb=" N HIS F 26 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY F 23 " --> pdb=" O GLY E 6 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD1, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD2, first strand: chain 'E' and resid 40 through 44 removed outlier: 8.232A pdb=" N LEU E 41 " --> pdb=" O CYS E 275 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR E 277 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER E 43 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.632A pdb=" N LEU E 50 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE E 79 " --> pdb=" O MET E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 110 through 115 removed outlier: 6.690A pdb=" N HIS E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE E 176 " --> pdb=" O HIS E 253 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 172 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 176 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 110 through 115 removed outlier: 6.690A pdb=" N HIS E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE E 176 " --> pdb=" O HIS E 253 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 172 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 133 through 138 removed outlier: 4.843A pdb=" N CYS E 136 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 161 through 166 Processing sheet with id=AD8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.788A pdb=" N CYS E 279 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR F 64 " --> pdb=" O GLY E 301 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1257 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: 1.81 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1895 1.27 - 1.41: 2984 1.41 - 1.55: 6604 1.55 - 1.68: 9 1.68 - 1.82: 72 Bond restraints: 11564 Sorted by residual: bond pdb=" CA ARG B 127 " pdb=" C ARG B 127 " ideal model delta sigma weight residual 1.523 1.413 0.111 1.34e-02 5.57e+03 6.80e+01 bond pdb=" CA ARG D 127 " pdb=" C ARG D 127 " ideal model delta sigma weight residual 1.529 1.453 0.076 9.30e-03 1.16e+04 6.72e+01 bond pdb=" C ASN C 320 " pdb=" O ASN C 320 " ideal model delta sigma weight residual 1.235 1.134 0.101 1.23e-02 6.61e+03 6.71e+01 bond pdb=" CA SER F 113 " pdb=" C SER F 113 " ideal model delta sigma weight residual 1.524 1.429 0.095 1.27e-02 6.20e+03 5.55e+01 bond pdb=" N ALA D 130 " pdb=" CA ALA D 130 " ideal model delta sigma weight residual 1.458 1.372 0.086 1.16e-02 7.43e+03 5.47e+01 ... (remaining 11559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 15398 2.42 - 4.85: 228 4.85 - 7.27: 35 7.27 - 9.70: 6 9.70 - 12.12: 2 Bond angle restraints: 15669 Sorted by residual: angle pdb=" N ASN B 129 " pdb=" CA ASN B 129 " pdb=" C ASN B 129 " ideal model delta sigma weight residual 112.30 102.03 10.27 1.36e+00 5.41e-01 5.70e+01 angle pdb=" C ARG D 127 " pdb=" CA ARG D 127 " pdb=" CB ARG D 127 " ideal model delta sigma weight residual 116.54 109.25 7.29 1.15e+00 7.56e-01 4.02e+01 angle pdb=" N GLY D 4 " pdb=" CA GLY D 4 " pdb=" C GLY D 4 " ideal model delta sigma weight residual 115.30 122.75 -7.45 1.39e+00 5.18e-01 2.87e+01 angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 112.86 119.23 -6.37 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N GLY B 8 " pdb=" CA GLY B 8 " pdb=" C GLY B 8 " ideal model delta sigma weight residual 113.18 101.06 12.12 2.37e+00 1.78e-01 2.62e+01 ... (remaining 15664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5673 17.64 - 35.28: 851 35.28 - 52.91: 292 52.91 - 70.55: 54 70.55 - 88.19: 16 Dihedral angle restraints: 6886 sinusoidal: 2764 harmonic: 4122 Sorted by residual: dihedral pdb=" C ASN B 128 " pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" CB ASN B 128 " ideal model delta harmonic sigma weight residual -122.60 -139.60 17.00 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 40.87 52.13 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CA ASN B 128 " pdb=" CB ASN B 128 " ideal model delta harmonic sigma weight residual 122.80 137.05 -14.25 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 6883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1670 0.151 - 0.301: 21 0.301 - 0.452: 8 0.452 - 0.603: 3 0.603 - 0.753: 1 Chirality restraints: 1703 Sorted by residual: chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA GLN B 125 " pdb=" N GLN B 125 " pdb=" C GLN B 125 " pdb=" CB GLN B 125 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA PHE B 3 " pdb=" N PHE B 3 " pdb=" C PHE B 3 " pdb=" CB PHE B 3 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 ... (remaining 1700 not shown) Planarity restraints: 2023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 113 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C SER D 113 " -0.064 2.00e-02 2.50e+03 pdb=" O SER D 113 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN D 114 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 123 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" C LYS D 123 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS D 123 " -0.020 2.00e-02 2.50e+03 pdb=" N SER D 124 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 217 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO E 218 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 218 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 218 " 0.034 5.00e-02 4.00e+02 ... (remaining 2020 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 612 2.71 - 3.26: 10360 3.26 - 3.80: 18230 3.80 - 4.35: 22325 4.35 - 4.90: 39277 Nonbonded interactions: 90804 Sorted by model distance: nonbonded pdb=" OD1 ASN D 28 " pdb=" N GLU D 29 " model vdw 2.162 3.120 nonbonded pdb=" N GLU E 99 " pdb=" OE1 GLU E 99 " model vdw 2.200 3.120 nonbonded pdb=" N GLU F 147 " pdb=" OE1 GLU F 147 " model vdw 2.219 3.120 nonbonded pdb=" OD1 ASP A 238 " pdb=" N THR A 239 " model vdw 2.240 3.120 nonbonded pdb=" O CYS C 42 " pdb=" OH TYR C 78 " model vdw 2.244 3.040 ... (remaining 90799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = (chain 'E' and resid 1 through 321) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 2 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 157)) selection = (chain 'F' and (resid 2 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 157)) } 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 group one per residue 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: 2.180 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 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 : 0.009 0.111 11583 Z= 0.572 Angle : 0.746 12.121 15708 Z= 0.439 Chirality : 0.063 0.753 1703 Planarity : 0.005 0.061 2022 Dihedral : 18.847 88.188 4198 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.17 % Allowed : 34.64 % Favored : 61.19 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1419 helix: 1.41 (0.28), residues: 351 sheet: -0.09 (0.33), residues: 264 loop : -1.52 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 217 TYR 0.018 0.002 TYR A 145 PHE 0.029 0.002 PHE F 3 TRP 0.011 0.001 TRP A 60 HIS 0.011 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00915 (11564) covalent geometry : angle 0.74508 (15669) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.10683 ( 36) hydrogen bonds : bond 0.15315 ( 437) hydrogen bonds : angle 6.24949 ( 1257) link_NAG-ASN : bond 0.00309 ( 1) link_NAG-ASN : angle 0.84195 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 353 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.8364 (m) cc_final: 0.8101 (p) REVERT: A 205 LYS cc_start: 0.7649 (mttp) cc_final: 0.7415 (mttp) REVERT: A 211 THR cc_start: 0.7917 (m) cc_final: 0.7672 (t) REVERT: A 227 MET cc_start: 0.6927 (mtt) cc_final: 0.6724 (mtt) REVERT: A 305 LYS cc_start: 0.8103 (mptp) cc_final: 0.7814 (mptp) REVERT: B 132 GLU cc_start: 0.6409 (tt0) cc_final: 0.6184 (tt0) REVERT: C 12 SER cc_start: 0.8079 (t) cc_final: 0.7664 (p) REVERT: C 22 LYS cc_start: 0.8701 (mttt) cc_final: 0.8338 (mtpt) REVERT: C 23 ASN cc_start: 0.8138 (m-40) cc_final: 0.7851 (t0) REVERT: C 149 LEU cc_start: 0.7972 (tp) cc_final: 0.7715 (tp) REVERT: C 227 MET cc_start: 0.7201 (mtt) cc_final: 0.6918 (mtt) REVERT: C 229 TYR cc_start: 0.8209 (m-80) cc_final: 0.7965 (m-10) REVERT: C 258 LYS cc_start: 0.6923 (tppp) cc_final: 0.6462 (tppp) REVERT: C 266 MET cc_start: 0.7279 (mtp) cc_final: 0.6980 (mtp) REVERT: C 300 ILE cc_start: 0.6204 (mt) cc_final: 0.5921 (mt) REVERT: C 305 LYS cc_start: 0.8111 (mptp) cc_final: 0.7801 (mptp) REVERT: D 50 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7230 (t0) REVERT: D 53 ASN cc_start: 0.8393 (m-40) cc_final: 0.8124 (m-40) REVERT: E 22 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7909 (mtmm) REVERT: E 113 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8237 (mtp180) REVERT: F 77 MET cc_start: 0.6783 (mmm) cc_final: 0.6531 (tpp) outliers start: 52 outliers final: 17 residues processed: 391 average time/residue: 0.1060 time to fit residues: 58.3629 Evaluate side-chains 333 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 315 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 30 GLN B 50 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 125 GLN D 129 ASN D 135 ASN E 31 ASN E 54 ASN E 180 HIS E 189 GLN E 228 ASN E 280 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125428 restraints weight = 16759.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130399 restraints weight = 8258.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133681 restraints weight = 4916.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135957 restraints weight = 3292.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137525 restraints weight = 2354.299| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11583 Z= 0.212 Angle : 0.642 6.049 15708 Z= 0.349 Chirality : 0.045 0.178 1703 Planarity : 0.004 0.046 2022 Dihedral : 6.693 56.334 1587 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.90 % Allowed : 31.60 % Favored : 61.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1419 helix: 1.96 (0.28), residues: 354 sheet: 0.38 (0.37), residues: 222 loop : -1.55 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 217 TYR 0.020 0.002 TYR B 119 PHE 0.014 0.002 PHE E 292 TRP 0.014 0.002 TRP E 231 HIS 0.007 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00451 (11564) covalent geometry : angle 0.64002 (15669) SS BOND : bond 0.00532 ( 18) SS BOND : angle 1.09804 ( 36) hydrogen bonds : bond 0.05774 ( 437) hydrogen bonds : angle 4.74513 ( 1257) link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 1.41204 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 375 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7053 (pt0) cc_final: 0.6844 (pt0) REVERT: A 44 LEU cc_start: 0.8545 (tp) cc_final: 0.8340 (tt) REVERT: A 112 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: A 119 LYS cc_start: 0.8624 (tttt) cc_final: 0.8217 (tptp) REVERT: A 171 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7821 (mtpt) REVERT: A 188 GLN cc_start: 0.7518 (tp40) cc_final: 0.7145 (tt0) REVERT: A 193 GLN cc_start: 0.8069 (tp40) cc_final: 0.7290 (tp40) REVERT: A 201 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7578 (p) REVERT: A 205 LYS cc_start: 0.8660 (mttp) cc_final: 0.8318 (mttp) REVERT: A 278 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7631 (ttmm) REVERT: A 290 LEU cc_start: 0.7523 (mt) cc_final: 0.7099 (mp) REVERT: A 305 LYS cc_start: 0.7811 (mptp) cc_final: 0.7466 (mptp) REVERT: B 53 ASN cc_start: 0.8574 (m-40) cc_final: 0.8354 (m110) REVERT: B 81 ASN cc_start: 0.7964 (t0) cc_final: 0.7653 (t0) REVERT: B 104 ASN cc_start: 0.8128 (m-40) cc_final: 0.7482 (m110) REVERT: B 140 PHE cc_start: 0.7906 (m-80) cc_final: 0.7492 (m-10) REVERT: B 149 MET cc_start: 0.7251 (mmt) cc_final: 0.6835 (mmt) REVERT: C 15 THR cc_start: 0.8587 (m) cc_final: 0.8155 (p) REVERT: C 22 LYS cc_start: 0.8335 (mttt) cc_final: 0.7992 (mtpt) REVERT: C 62 LEU cc_start: 0.7534 (mt) cc_final: 0.7249 (mm) REVERT: C 66 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8646 (mmmt) REVERT: C 100 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6663 (mm-30) REVERT: C 147 ASN cc_start: 0.8033 (m-40) cc_final: 0.7535 (m110) REVERT: C 154 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7627 (ttmm) REVERT: C 164 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 207 TYR cc_start: 0.8112 (t80) cc_final: 0.7872 (t80) REVERT: C 219 LYS cc_start: 0.7580 (mtpp) cc_final: 0.7250 (mtpp) REVERT: C 227 MET cc_start: 0.7213 (mtt) cc_final: 0.6988 (mtt) REVERT: C 229 TYR cc_start: 0.8440 (m-80) cc_final: 0.8086 (m-10) REVERT: C 243 GLU cc_start: 0.6858 (tt0) cc_final: 0.6417 (tt0) REVERT: C 266 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6567 (mtp) REVERT: C 300 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7651 (mt) REVERT: C 305 LYS cc_start: 0.7676 (mptp) cc_final: 0.7332 (mptp) REVERT: C 308 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7769 (mtpp) REVERT: D 53 ASN cc_start: 0.8375 (m-40) cc_final: 0.8000 (m-40) REVERT: D 128 ASN cc_start: 0.7793 (p0) cc_final: 0.7529 (p0) REVERT: D 140 PHE cc_start: 0.7923 (m-80) cc_final: 0.7371 (m-10) REVERT: E 3 ILE cc_start: 0.7587 (tt) cc_final: 0.7339 (pt) REVERT: E 23 ASN cc_start: 0.8153 (t0) cc_final: 0.7606 (t0) REVERT: E 48 ILE cc_start: 0.6694 (mm) cc_final: 0.6470 (tt) REVERT: E 77 SER cc_start: 0.8407 (t) cc_final: 0.8090 (p) REVERT: E 102 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7427 (ttmm) REVERT: E 133 THR cc_start: 0.7952 (p) cc_final: 0.7698 (p) REVERT: E 143 SER cc_start: 0.8164 (t) cc_final: 0.7870 (p) REVERT: E 147 ASN cc_start: 0.7845 (m-40) cc_final: 0.7240 (m110) REVERT: E 172 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: E 188 GLN cc_start: 0.7837 (tp40) cc_final: 0.6950 (tp40) REVERT: E 192 TYR cc_start: 0.7573 (m-80) cc_final: 0.7318 (m-10) REVERT: E 197 THR cc_start: 0.8269 (p) cc_final: 0.7783 (t) REVERT: E 201 VAL cc_start: 0.8269 (t) cc_final: 0.7708 (p) REVERT: E 205 LYS cc_start: 0.8273 (mttm) cc_final: 0.8020 (mtpm) REVERT: E 243 GLU cc_start: 0.6925 (tt0) cc_final: 0.6448 (tt0) REVERT: E 305 LYS cc_start: 0.7763 (mptt) cc_final: 0.7481 (mptt) REVERT: F 53 ASN cc_start: 0.8209 (m-40) cc_final: 0.7879 (m-40) REVERT: F 81 ASN cc_start: 0.7963 (t0) cc_final: 0.7755 (t0) outliers start: 86 outliers final: 39 residues processed: 417 average time/residue: 0.1084 time to fit residues: 63.2786 Evaluate side-chains 399 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 354 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 114 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS B 125 GLN C 8 HIS C 196 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125101 restraints weight = 16744.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130083 restraints weight = 8197.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133419 restraints weight = 4873.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135640 restraints weight = 3229.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137283 restraints weight = 2319.969| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11583 Z= 0.126 Angle : 0.525 7.571 15708 Z= 0.281 Chirality : 0.042 0.190 1703 Planarity : 0.004 0.046 2022 Dihedral : 5.295 57.577 1566 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.53 % Allowed : 33.60 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1419 helix: 2.64 (0.29), residues: 354 sheet: 0.54 (0.38), residues: 222 loop : -1.48 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 217 TYR 0.013 0.001 TYR C 306 PHE 0.017 0.001 PHE F 138 TRP 0.009 0.001 TRP C 252 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00263 (11564) covalent geometry : angle 0.52383 (15669) SS BOND : bond 0.00857 ( 18) SS BOND : angle 0.90096 ( 36) hydrogen bonds : bond 0.04648 ( 437) hydrogen bonds : angle 4.34574 ( 1257) link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 1.03284 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 369 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 VAL cc_start: 0.8426 (t) cc_final: 0.8220 (m) REVERT: A 22 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7812 (mtpp) REVERT: A 66 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8397 (mmmt) REVERT: A 119 LYS cc_start: 0.8591 (tttt) cc_final: 0.8248 (tptt) REVERT: A 121 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7232 (p) REVERT: A 135 SER cc_start: 0.8026 (t) cc_final: 0.7793 (t) REVERT: A 171 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7661 (mtpt) REVERT: A 177 TRP cc_start: 0.8561 (p90) cc_final: 0.8336 (p90) REVERT: A 188 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: A 193 GLN cc_start: 0.7892 (tp40) cc_final: 0.7547 (tp40) REVERT: A 201 VAL cc_start: 0.7909 (t) cc_final: 0.7456 (p) REVERT: A 205 LYS cc_start: 0.8605 (mttp) cc_final: 0.8250 (mttp) REVERT: A 278 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7577 (ttmm) REVERT: A 290 LEU cc_start: 0.7491 (mt) cc_final: 0.7027 (mp) REVERT: A 305 LYS cc_start: 0.7848 (mptp) cc_final: 0.7479 (mptp) REVERT: B 11 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6131 (pp20) REVERT: B 50 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 81 ASN cc_start: 0.7820 (t0) cc_final: 0.7493 (t0) REVERT: B 140 PHE cc_start: 0.7809 (m-80) cc_final: 0.7426 (m-10) REVERT: B 149 MET cc_start: 0.7252 (mmt) cc_final: 0.6914 (mmp) REVERT: C 8 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7174 (t-170) REVERT: C 15 THR cc_start: 0.8532 (m) cc_final: 0.8115 (p) REVERT: C 43 SER cc_start: 0.7969 (m) cc_final: 0.7689 (t) REVERT: C 62 LEU cc_start: 0.7626 (mt) cc_final: 0.7315 (mm) REVERT: C 66 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8594 (mmmt) REVERT: C 108 VAL cc_start: 0.8742 (t) cc_final: 0.8509 (p) REVERT: C 147 ASN cc_start: 0.8036 (m-40) cc_final: 0.7651 (m110) REVERT: C 154 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7614 (ttmm) REVERT: C 156 ASN cc_start: 0.8409 (p0) cc_final: 0.8194 (p0) REVERT: C 177 TRP cc_start: 0.8535 (p90) cc_final: 0.8290 (p90) REVERT: C 219 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7503 (mtpp) REVERT: C 227 MET cc_start: 0.7134 (mtt) cc_final: 0.6895 (mtt) REVERT: C 229 TYR cc_start: 0.8460 (m-80) cc_final: 0.8103 (m-10) REVERT: C 243 GLU cc_start: 0.6774 (tt0) cc_final: 0.6371 (tt0) REVERT: C 266 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6196 (mtp) REVERT: C 305 LYS cc_start: 0.7674 (mptp) cc_final: 0.7323 (mptp) REVERT: C 308 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7818 (mtpp) REVERT: D 53 ASN cc_start: 0.8326 (m-40) cc_final: 0.7947 (m110) REVERT: D 81 ASN cc_start: 0.7789 (t0) cc_final: 0.7587 (t0) REVERT: D 140 PHE cc_start: 0.8023 (m-80) cc_final: 0.7812 (m-10) REVERT: E 3 ILE cc_start: 0.7528 (tt) cc_final: 0.7305 (mp) REVERT: E 23 ASN cc_start: 0.8093 (t0) cc_final: 0.7537 (t0) REVERT: E 100 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6608 (mm-30) REVERT: E 102 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7426 (ttmm) REVERT: E 112 GLU cc_start: 0.7173 (tt0) cc_final: 0.6928 (tt0) REVERT: E 115 GLU cc_start: 0.6838 (tt0) cc_final: 0.6568 (tt0) REVERT: E 147 ASN cc_start: 0.7836 (m-40) cc_final: 0.7393 (m110) REVERT: E 172 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: E 189 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7304 (tp-100) REVERT: E 197 THR cc_start: 0.8327 (p) cc_final: 0.7909 (t) REVERT: E 198 TYR cc_start: 0.8540 (p90) cc_final: 0.8294 (p90) REVERT: E 201 VAL cc_start: 0.8214 (t) cc_final: 0.7663 (p) REVERT: E 205 LYS cc_start: 0.8146 (mttm) cc_final: 0.7910 (mtpm) REVERT: E 276 THR cc_start: 0.7197 (t) cc_final: 0.6632 (p) REVERT: E 305 LYS cc_start: 0.7827 (mptt) cc_final: 0.7533 (mptt) REVERT: F 24 TYR cc_start: 0.8325 (m-80) cc_final: 0.8053 (m-10) REVERT: F 53 ASN cc_start: 0.8175 (m-40) cc_final: 0.7826 (m110) REVERT: F 81 ASN cc_start: 0.7816 (t0) cc_final: 0.7572 (t0) REVERT: F 138 PHE cc_start: 0.8059 (m-80) cc_final: 0.7821 (m-10) outliers start: 69 outliers final: 36 residues processed: 402 average time/residue: 0.1162 time to fit residues: 64.9380 Evaluate side-chains 407 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 114 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN E 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119211 restraints weight = 16947.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124146 restraints weight = 8115.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127363 restraints weight = 4778.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129614 restraints weight = 3192.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131183 restraints weight = 2275.967| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11583 Z= 0.237 Angle : 0.607 9.263 15708 Z= 0.325 Chirality : 0.044 0.181 1703 Planarity : 0.004 0.050 2022 Dihedral : 5.477 55.720 1565 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 7.30 % Allowed : 32.64 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1419 helix: 2.52 (0.28), residues: 351 sheet: 0.71 (0.33), residues: 297 loop : -1.72 (0.19), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 313 TYR 0.020 0.002 TYR C 7 PHE 0.017 0.002 PHE E 111 TRP 0.012 0.002 TRP E 231 HIS 0.007 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00502 (11564) covalent geometry : angle 0.60537 (15669) SS BOND : bond 0.00398 ( 18) SS BOND : angle 0.96942 ( 36) hydrogen bonds : bond 0.05992 ( 437) hydrogen bonds : angle 4.57534 ( 1257) link_NAG-ASN : bond 0.00222 ( 1) link_NAG-ASN : angle 1.78772 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 410 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.8687 (t) cc_final: 0.8384 (p) REVERT: A 34 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5990 (mt-10) REVERT: A 119 LYS cc_start: 0.8664 (tttt) cc_final: 0.8367 (tptt) REVERT: A 123 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.8039 (m100) REVERT: A 135 SER cc_start: 0.8196 (t) cc_final: 0.7971 (t) REVERT: A 157 SER cc_start: 0.8114 (t) cc_final: 0.7697 (m) REVERT: A 161 LEU cc_start: 0.7865 (tt) cc_final: 0.7391 (tt) REVERT: A 171 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7715 (mtpt) REVERT: A 188 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: A 193 GLN cc_start: 0.7933 (tp40) cc_final: 0.7585 (tp40) REVERT: A 201 VAL cc_start: 0.8120 (t) cc_final: 0.7671 (p) REVERT: A 204 THR cc_start: 0.8271 (m) cc_final: 0.7879 (p) REVERT: A 205 LYS cc_start: 0.8720 (mttp) cc_final: 0.8438 (mttp) REVERT: A 278 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7808 (ttmm) REVERT: A 290 LEU cc_start: 0.7592 (mt) cc_final: 0.7249 (mp) REVERT: A 305 LYS cc_start: 0.7900 (mptp) cc_final: 0.7516 (mptp) REVERT: B 11 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6502 (pp20) REVERT: B 39 LYS cc_start: 0.8384 (tttp) cc_final: 0.8168 (tttp) REVERT: B 81 ASN cc_start: 0.8028 (t0) cc_final: 0.7720 (t0) REVERT: B 131 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7418 (ttpp) REVERT: B 140 PHE cc_start: 0.7660 (m-80) cc_final: 0.7400 (m-10) REVERT: B 149 MET cc_start: 0.7474 (mmt) cc_final: 0.7023 (mmp) REVERT: B 153 LYS cc_start: 0.8608 (mttt) cc_final: 0.8380 (mttt) REVERT: C 15 THR cc_start: 0.8561 (m) cc_final: 0.8193 (p) REVERT: C 43 SER cc_start: 0.8295 (m) cc_final: 0.7977 (t) REVERT: C 66 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8308 (mptt) REVERT: C 111 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: C 112 GLU cc_start: 0.7289 (tt0) cc_final: 0.6948 (mt-10) REVERT: C 147 ASN cc_start: 0.8062 (m-40) cc_final: 0.7572 (m110) REVERT: C 154 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7687 (ttmm) REVERT: C 156 ASN cc_start: 0.8498 (p0) cc_final: 0.8157 (p0) REVERT: C 177 TRP cc_start: 0.8569 (p90) cc_final: 0.8348 (p90) REVERT: C 201 VAL cc_start: 0.8126 (t) cc_final: 0.7617 (p) REVERT: C 205 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7976 (mtmm) REVERT: C 207 TYR cc_start: 0.7978 (t80) cc_final: 0.7628 (t80) REVERT: C 219 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7717 (mtpt) REVERT: C 227 MET cc_start: 0.7130 (mtt) cc_final: 0.6918 (mtt) REVERT: C 229 TYR cc_start: 0.8465 (m-80) cc_final: 0.8037 (m-10) REVERT: C 257 LEU cc_start: 0.8363 (mp) cc_final: 0.8032 (mt) REVERT: C 258 LYS cc_start: 0.7319 (tppp) cc_final: 0.6932 (tppp) REVERT: C 266 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6127 (mtp) REVERT: C 305 LYS cc_start: 0.7712 (mptp) cc_final: 0.7411 (mptp) REVERT: D 53 ASN cc_start: 0.8333 (m-40) cc_final: 0.7976 (m110) REVERT: D 117 ASN cc_start: 0.8138 (m-40) cc_final: 0.7902 (m110) REVERT: D 140 PHE cc_start: 0.7940 (m-80) cc_final: 0.7611 (m-10) REVERT: E 23 ASN cc_start: 0.8062 (t0) cc_final: 0.7529 (t0) REVERT: E 38 ASN cc_start: 0.7673 (p0) cc_final: 0.7256 (p0) REVERT: E 62 LEU cc_start: 0.7502 (mt) cc_final: 0.6964 (mm) REVERT: E 81 GLU cc_start: 0.7056 (tt0) cc_final: 0.6814 (tt0) REVERT: E 87 ASN cc_start: 0.8006 (m-40) cc_final: 0.7596 (m-40) REVERT: E 100 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6723 (mm-30) REVERT: E 102 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7429 (ttmm) REVERT: E 115 GLU cc_start: 0.6828 (tt0) cc_final: 0.6538 (tt0) REVERT: E 147 ASN cc_start: 0.7958 (m110) cc_final: 0.7360 (m110) REVERT: E 153 LYS cc_start: 0.8316 (pptt) cc_final: 0.8091 (pptt) REVERT: E 154 LYS cc_start: 0.8376 (tptt) cc_final: 0.8097 (tptt) REVERT: E 171 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7569 (mmtp) REVERT: E 198 TYR cc_start: 0.8645 (p90) cc_final: 0.8432 (p90) REVERT: E 201 VAL cc_start: 0.8232 (t) cc_final: 0.7811 (p) REVERT: E 205 LYS cc_start: 0.8314 (mttm) cc_final: 0.7967 (mtpm) REVERT: E 278 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8038 (tttp) REVERT: E 293 GLN cc_start: 0.7905 (pp30) cc_final: 0.7609 (pt0) REVERT: E 318 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6979 (pp) REVERT: F 53 ASN cc_start: 0.8184 (m-40) cc_final: 0.7981 (m110) REVERT: F 59 MET cc_start: 0.7544 (tpp) cc_final: 0.7253 (mpp) REVERT: F 81 ASN cc_start: 0.8039 (t0) cc_final: 0.7793 (t0) REVERT: F 143 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7776 (tppp) REVERT: F 153 LYS cc_start: 0.8379 (mttt) cc_final: 0.8069 (mttt) outliers start: 91 outliers final: 60 residues processed: 453 average time/residue: 0.1211 time to fit residues: 74.8651 Evaluate side-chains 466 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121733 restraints weight = 16546.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126613 restraints weight = 8084.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129813 restraints weight = 4817.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132026 restraints weight = 3230.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133567 restraints weight = 2317.111| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11583 Z= 0.129 Angle : 0.529 7.249 15708 Z= 0.278 Chirality : 0.041 0.181 1703 Planarity : 0.004 0.068 2022 Dihedral : 4.865 56.043 1564 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.13 % Allowed : 34.96 % Favored : 59.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1419 helix: 2.94 (0.28), residues: 351 sheet: 0.53 (0.35), residues: 261 loop : -1.54 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.019 0.002 TYR A 306 PHE 0.012 0.001 PHE E 111 TRP 0.007 0.001 TRP D 14 HIS 0.010 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00273 (11564) covalent geometry : angle 0.52906 (15669) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.63617 ( 36) hydrogen bonds : bond 0.04663 ( 437) hydrogen bonds : angle 4.23772 ( 1257) link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 0.99894 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 365 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.8694 (t) cc_final: 0.8419 (p) REVERT: A 34 GLU cc_start: 0.6138 (mt-10) cc_final: 0.5868 (mt-10) REVERT: A 84 ASN cc_start: 0.7846 (t0) cc_final: 0.7056 (t0) REVERT: A 119 LYS cc_start: 0.8522 (tttt) cc_final: 0.8249 (tttp) REVERT: A 123 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7891 (m100) REVERT: A 157 SER cc_start: 0.8174 (t) cc_final: 0.7801 (m) REVERT: A 171 LYS cc_start: 0.7869 (ptpt) cc_final: 0.7574 (mtpt) REVERT: A 188 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: A 193 GLN cc_start: 0.7893 (tp40) cc_final: 0.7527 (tp40) REVERT: A 201 VAL cc_start: 0.8001 (t) cc_final: 0.7533 (p) REVERT: A 204 THR cc_start: 0.8190 (m) cc_final: 0.7822 (p) REVERT: A 205 LYS cc_start: 0.8611 (mttp) cc_final: 0.8341 (mttp) REVERT: A 278 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7782 (ttmm) REVERT: A 290 LEU cc_start: 0.7478 (mt) cc_final: 0.7085 (mp) REVERT: A 305 LYS cc_start: 0.7809 (mptp) cc_final: 0.7435 (mptp) REVERT: B 11 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6387 (pp20) REVERT: B 81 ASN cc_start: 0.7917 (t0) cc_final: 0.7612 (t0) REVERT: C 15 THR cc_start: 0.8541 (m) cc_final: 0.8148 (p) REVERT: C 43 SER cc_start: 0.8253 (m) cc_final: 0.7860 (p) REVERT: C 66 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8355 (mmtt) REVERT: C 111 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7917 (m-10) REVERT: C 112 GLU cc_start: 0.7212 (tt0) cc_final: 0.6919 (mt-10) REVERT: C 147 ASN cc_start: 0.8050 (m-40) cc_final: 0.7646 (m110) REVERT: C 154 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7607 (ttmm) REVERT: C 156 ASN cc_start: 0.8427 (p0) cc_final: 0.8094 (p0) REVERT: C 201 VAL cc_start: 0.8128 (t) cc_final: 0.7643 (p) REVERT: C 205 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7908 (mtmm) REVERT: C 229 TYR cc_start: 0.8492 (m-80) cc_final: 0.8092 (m-10) REVERT: C 257 LEU cc_start: 0.8321 (mp) cc_final: 0.8009 (mt) REVERT: C 258 LYS cc_start: 0.7242 (tppp) cc_final: 0.6898 (tppp) REVERT: C 266 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.6091 (mtp) REVERT: C 305 LYS cc_start: 0.7650 (mptp) cc_final: 0.7399 (mptp) REVERT: D 117 ASN cc_start: 0.7974 (m-40) cc_final: 0.7753 (m-40) REVERT: D 139 GLU cc_start: 0.7264 (tt0) cc_final: 0.7036 (tt0) REVERT: D 140 PHE cc_start: 0.7913 (m-80) cc_final: 0.7666 (m-10) REVERT: E 23 ASN cc_start: 0.8035 (t0) cc_final: 0.7496 (t0) REVERT: E 38 ASN cc_start: 0.7664 (p0) cc_final: 0.7325 (p0) REVERT: E 87 ASN cc_start: 0.8002 (m-40) cc_final: 0.7691 (m-40) REVERT: E 100 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6679 (mm-30) REVERT: E 102 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7450 (ttmm) REVERT: E 115 GLU cc_start: 0.6805 (tt0) cc_final: 0.6516 (tt0) REVERT: E 147 ASN cc_start: 0.7878 (m110) cc_final: 0.7194 (m110) REVERT: E 154 LYS cc_start: 0.8334 (tptt) cc_final: 0.8012 (tptt) REVERT: E 191 LEU cc_start: 0.8215 (mm) cc_final: 0.7877 (mt) REVERT: E 197 THR cc_start: 0.8373 (p) cc_final: 0.7892 (t) REVERT: E 198 TYR cc_start: 0.8625 (p90) cc_final: 0.8350 (p90) REVERT: E 201 VAL cc_start: 0.8201 (t) cc_final: 0.7745 (p) REVERT: E 205 LYS cc_start: 0.8215 (mttm) cc_final: 0.7882 (mtpm) REVERT: E 211 THR cc_start: 0.7900 (m) cc_final: 0.7559 (t) REVERT: E 293 GLN cc_start: 0.7846 (pp30) cc_final: 0.7557 (pt0) REVERT: F 53 ASN cc_start: 0.8251 (m-40) cc_final: 0.7900 (m110) REVERT: F 81 ASN cc_start: 0.7895 (t0) cc_final: 0.7632 (t0) outliers start: 64 outliers final: 41 residues processed: 396 average time/residue: 0.1169 time to fit residues: 63.8965 Evaluate side-chains 408 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 362 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 128 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN C 147 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN F 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119160 restraints weight = 16813.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124059 restraints weight = 8144.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127270 restraints weight = 4802.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129500 restraints weight = 3185.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131066 restraints weight = 2262.857| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11583 Z= 0.175 Angle : 0.553 8.535 15708 Z= 0.290 Chirality : 0.042 0.180 1703 Planarity : 0.004 0.066 2022 Dihedral : 4.737 51.757 1559 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.42 % Allowed : 34.72 % Favored : 58.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1419 helix: 2.99 (0.28), residues: 351 sheet: 0.52 (0.35), residues: 246 loop : -1.47 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.020 0.002 TYR A 306 PHE 0.016 0.002 PHE E 111 TRP 0.008 0.001 TRP D 14 HIS 0.009 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00376 (11564) covalent geometry : angle 0.55187 (15669) SS BOND : bond 0.00297 ( 18) SS BOND : angle 0.78204 ( 36) hydrogen bonds : bond 0.05202 ( 437) hydrogen bonds : angle 4.31889 ( 1257) link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 1.28053 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 391 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.8720 (t) cc_final: 0.8465 (p) REVERT: A 84 ASN cc_start: 0.7937 (t0) cc_final: 0.7237 (t0) REVERT: A 119 LYS cc_start: 0.8547 (tttt) cc_final: 0.8288 (tttp) REVERT: A 123 TRP cc_start: 0.8574 (OUTLIER) cc_final: 0.7861 (m100) REVERT: A 157 SER cc_start: 0.8289 (t) cc_final: 0.7912 (m) REVERT: A 171 LYS cc_start: 0.7891 (ptpt) cc_final: 0.7568 (mtpt) REVERT: A 188 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: A 193 GLN cc_start: 0.7869 (tp40) cc_final: 0.7433 (tp40) REVERT: A 201 VAL cc_start: 0.8055 (t) cc_final: 0.7628 (p) REVERT: A 204 THR cc_start: 0.8226 (m) cc_final: 0.7869 (p) REVERT: A 205 LYS cc_start: 0.8637 (mttp) cc_final: 0.8394 (mttp) REVERT: A 278 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7868 (ttmm) REVERT: A 305 LYS cc_start: 0.7813 (mptp) cc_final: 0.7448 (mptp) REVERT: B 81 ASN cc_start: 0.7897 (t0) cc_final: 0.7578 (t0) REVERT: B 140 PHE cc_start: 0.7950 (m-10) cc_final: 0.7737 (m-10) REVERT: C 15 THR cc_start: 0.8560 (m) cc_final: 0.8200 (p) REVERT: C 43 SER cc_start: 0.8351 (m) cc_final: 0.8002 (t) REVERT: C 66 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8344 (mmtt) REVERT: C 111 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8097 (m-10) REVERT: C 147 ASN cc_start: 0.8055 (m110) cc_final: 0.7627 (m110) REVERT: C 149 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7880 (tp) REVERT: C 154 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7688 (ttmm) REVERT: C 156 ASN cc_start: 0.8396 (p0) cc_final: 0.8059 (p0) REVERT: C 201 VAL cc_start: 0.8117 (t) cc_final: 0.7656 (p) REVERT: C 205 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8040 (mtmm) REVERT: C 229 TYR cc_start: 0.8475 (m-80) cc_final: 0.8050 (m-10) REVERT: C 257 LEU cc_start: 0.8327 (mp) cc_final: 0.8001 (mt) REVERT: C 258 LYS cc_start: 0.7287 (tppp) cc_final: 0.6947 (tppp) REVERT: C 266 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6073 (mtp) REVERT: C 305 LYS cc_start: 0.7624 (mptp) cc_final: 0.7393 (mptp) REVERT: D 52 VAL cc_start: 0.8393 (t) cc_final: 0.8110 (p) REVERT: D 139 GLU cc_start: 0.7269 (tt0) cc_final: 0.7020 (tt0) REVERT: E 23 ASN cc_start: 0.8024 (t0) cc_final: 0.7483 (t0) REVERT: E 38 ASN cc_start: 0.7846 (p0) cc_final: 0.7548 (p0) REVERT: E 62 LEU cc_start: 0.7446 (mt) cc_final: 0.6844 (mm) REVERT: E 87 ASN cc_start: 0.8055 (m-40) cc_final: 0.7766 (m-40) REVERT: E 100 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6698 (mm-30) REVERT: E 102 LYS cc_start: 0.7784 (mtmt) cc_final: 0.7401 (ttmm) REVERT: E 115 GLU cc_start: 0.6816 (tt0) cc_final: 0.6518 (tt0) REVERT: E 119 LYS cc_start: 0.8444 (ptmt) cc_final: 0.7938 (ttmt) REVERT: E 147 ASN cc_start: 0.7874 (m110) cc_final: 0.7180 (m110) REVERT: E 148 LEU cc_start: 0.8212 (mp) cc_final: 0.7998 (mm) REVERT: E 154 LYS cc_start: 0.8395 (tptt) cc_final: 0.8063 (tptt) REVERT: E 191 LEU cc_start: 0.8266 (mm) cc_final: 0.7896 (mp) REVERT: E 197 THR cc_start: 0.8347 (p) cc_final: 0.7791 (t) REVERT: E 198 TYR cc_start: 0.8639 (p90) cc_final: 0.8260 (p90) REVERT: E 201 VAL cc_start: 0.8235 (t) cc_final: 0.7783 (p) REVERT: E 205 LYS cc_start: 0.8286 (mttm) cc_final: 0.7937 (mtpm) REVERT: E 211 THR cc_start: 0.7899 (m) cc_final: 0.7390 (p) REVERT: E 293 GLN cc_start: 0.7856 (pp30) cc_final: 0.7593 (pt0) REVERT: E 305 LYS cc_start: 0.7786 (mptt) cc_final: 0.7464 (mptt) REVERT: F 11 GLU cc_start: 0.7501 (pt0) cc_final: 0.7198 (pt0) REVERT: F 53 ASN cc_start: 0.8181 (m-40) cc_final: 0.7889 (m110) REVERT: F 81 ASN cc_start: 0.7908 (t0) cc_final: 0.7673 (t0) REVERT: F 143 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7862 (tppp) REVERT: F 153 LYS cc_start: 0.8337 (mttt) cc_final: 0.8136 (mttt) outliers start: 80 outliers final: 60 residues processed: 429 average time/residue: 0.1206 time to fit residues: 71.3820 Evaluate side-chains 457 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 391 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 66 optimal weight: 0.0030 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN B 28 ASN B 71 ASN B 79 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120717 restraints weight = 16841.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125651 restraints weight = 8117.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128869 restraints weight = 4775.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131119 restraints weight = 3178.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132687 restraints weight = 2253.362| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11583 Z= 0.117 Angle : 0.531 10.120 15708 Z= 0.274 Chirality : 0.041 0.172 1703 Planarity : 0.003 0.061 2022 Dihedral : 4.554 51.854 1559 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.45 % Allowed : 35.85 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1419 helix: 3.23 (0.28), residues: 351 sheet: 0.53 (0.38), residues: 216 loop : -1.33 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.019 0.002 TYR E 192 PHE 0.013 0.001 PHE E 111 TRP 0.008 0.001 TRP A 177 HIS 0.008 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00250 (11564) covalent geometry : angle 0.53056 (15669) SS BOND : bond 0.00274 ( 18) SS BOND : angle 0.62008 ( 36) hydrogen bonds : bond 0.04494 ( 437) hydrogen bonds : angle 4.09547 ( 1257) link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 0.89713 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 384 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.8705 (t) cc_final: 0.8438 (p) REVERT: A 76 TRP cc_start: 0.8395 (p90) cc_final: 0.7697 (p90) REVERT: A 84 ASN cc_start: 0.7946 (t0) cc_final: 0.7252 (t0) REVERT: A 119 LYS cc_start: 0.8449 (tttt) cc_final: 0.8208 (tttp) REVERT: A 123 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.7692 (m100) REVERT: A 157 SER cc_start: 0.8290 (t) cc_final: 0.7928 (m) REVERT: A 171 LYS cc_start: 0.7772 (ptpt) cc_final: 0.7513 (mtpt) REVERT: A 188 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: A 193 GLN cc_start: 0.7874 (tp40) cc_final: 0.7442 (tp40) REVERT: A 204 THR cc_start: 0.8212 (m) cc_final: 0.7699 (p) REVERT: A 205 LYS cc_start: 0.8632 (mttp) cc_final: 0.8381 (mttp) REVERT: A 238 ASP cc_start: 0.6919 (t0) cc_final: 0.5748 (t0) REVERT: A 278 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7852 (ttmm) REVERT: A 305 LYS cc_start: 0.7744 (mptp) cc_final: 0.7363 (mptp) REVERT: B 11 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: B 71 ASN cc_start: 0.7871 (p0) cc_final: 0.7580 (p0) REVERT: B 81 ASN cc_start: 0.7836 (t0) cc_final: 0.7522 (t0) REVERT: C 5 VAL cc_start: 0.8457 (p) cc_final: 0.8213 (t) REVERT: C 15 THR cc_start: 0.8559 (m) cc_final: 0.8187 (p) REVERT: C 43 SER cc_start: 0.8310 (m) cc_final: 0.7897 (p) REVERT: C 66 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8338 (mmtt) REVERT: C 111 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: C 147 ASN cc_start: 0.8027 (m110) cc_final: 0.7579 (m110) REVERT: C 149 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (tp) REVERT: C 154 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7720 (ttmm) REVERT: C 156 ASN cc_start: 0.8355 (p0) cc_final: 0.7978 (p0) REVERT: C 172 GLU cc_start: 0.7070 (pt0) cc_final: 0.6795 (pt0) REVERT: C 205 LYS cc_start: 0.8259 (mtmm) cc_final: 0.8010 (mtmm) REVERT: C 229 TYR cc_start: 0.8432 (m-80) cc_final: 0.8037 (m-10) REVERT: C 257 LEU cc_start: 0.8279 (mp) cc_final: 0.7968 (mt) REVERT: C 266 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6052 (mtp) REVERT: C 305 LYS cc_start: 0.7575 (mptp) cc_final: 0.7369 (mptp) REVERT: D 27 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6532 (ttm110) REVERT: D 53 ASN cc_start: 0.8267 (m-40) cc_final: 0.8026 (m110) REVERT: D 139 GLU cc_start: 0.7217 (tt0) cc_final: 0.7015 (tt0) REVERT: D 147 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: E 23 ASN cc_start: 0.8017 (t0) cc_final: 0.7463 (t0) REVERT: E 38 ASN cc_start: 0.7800 (p0) cc_final: 0.7553 (p0) REVERT: E 75 SER cc_start: 0.8178 (m) cc_final: 0.7872 (p) REVERT: E 87 ASN cc_start: 0.8064 (m-40) cc_final: 0.7804 (m-40) REVERT: E 100 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6661 (mm-30) REVERT: E 102 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7338 (ttmm) REVERT: E 115 GLU cc_start: 0.6820 (tt0) cc_final: 0.6488 (tt0) REVERT: E 119 LYS cc_start: 0.8387 (ptmt) cc_final: 0.7908 (ttmt) REVERT: E 147 ASN cc_start: 0.7898 (m110) cc_final: 0.7246 (m110) REVERT: E 154 LYS cc_start: 0.8372 (tptt) cc_final: 0.8042 (tptt) REVERT: E 191 LEU cc_start: 0.8268 (mm) cc_final: 0.7909 (mp) REVERT: E 197 THR cc_start: 0.8408 (p) cc_final: 0.7849 (t) REVERT: E 198 TYR cc_start: 0.8638 (p90) cc_final: 0.8254 (p90) REVERT: E 201 VAL cc_start: 0.8211 (t) cc_final: 0.7728 (p) REVERT: E 205 LYS cc_start: 0.8239 (mttm) cc_final: 0.7888 (mtpm) REVERT: E 211 THR cc_start: 0.7816 (m) cc_final: 0.7317 (p) REVERT: E 293 GLN cc_start: 0.7855 (pp30) cc_final: 0.7538 (pt0) REVERT: F 11 GLU cc_start: 0.7455 (pt0) cc_final: 0.7234 (pt0) REVERT: F 53 ASN cc_start: 0.8150 (m-40) cc_final: 0.7863 (m110) REVERT: F 81 ASN cc_start: 0.7825 (t0) cc_final: 0.7589 (t0) REVERT: F 105 GLU cc_start: 0.7058 (tp30) cc_final: 0.6290 (tp30) REVERT: F 143 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7872 (tppp) outliers start: 68 outliers final: 48 residues processed: 418 average time/residue: 0.1197 time to fit residues: 68.9630 Evaluate side-chains 441 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 384 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 311 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 71 ASN E 31 ASN E 189 GLN F 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114813 restraints weight = 16909.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119507 restraints weight = 8122.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122621 restraints weight = 4784.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124730 restraints weight = 3176.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126301 restraints weight = 2277.058| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 11583 Z= 0.414 Angle : 0.718 9.631 15708 Z= 0.382 Chirality : 0.049 0.224 1703 Planarity : 0.004 0.073 2022 Dihedral : 5.297 46.519 1559 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 7.06 % Allowed : 34.80 % Favored : 58.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1419 helix: 2.40 (0.28), residues: 339 sheet: 0.49 (0.34), residues: 246 loop : -1.82 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 313 TYR 0.024 0.004 TYR E 192 PHE 0.031 0.003 PHE B 140 TRP 0.025 0.003 TRP A 76 HIS 0.010 0.002 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00883 (11564) covalent geometry : angle 0.71599 (15669) SS BOND : bond 0.00434 ( 18) SS BOND : angle 1.14528 ( 36) hydrogen bonds : bond 0.07125 ( 437) hydrogen bonds : angle 4.94921 ( 1257) link_NAG-ASN : bond 0.00583 ( 1) link_NAG-ASN : angle 2.42512 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 446 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8092 (t0) cc_final: 0.7574 (t0) REVERT: A 111 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: A 123 TRP cc_start: 0.8603 (OUTLIER) cc_final: 0.8042 (m100) REVERT: A 157 SER cc_start: 0.8414 (t) cc_final: 0.8071 (m) REVERT: A 188 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: A 193 GLN cc_start: 0.7863 (tp40) cc_final: 0.7516 (tp40) REVERT: A 201 VAL cc_start: 0.8195 (t) cc_final: 0.7782 (p) REVERT: A 204 THR cc_start: 0.8363 (m) cc_final: 0.7906 (p) REVERT: A 205 LYS cc_start: 0.8739 (mttp) cc_final: 0.8522 (mttp) REVERT: A 211 THR cc_start: 0.8282 (m) cc_final: 0.7921 (t) REVERT: A 230 TYR cc_start: 0.8201 (m-80) cc_final: 0.7946 (m-80) REVERT: A 238 ASP cc_start: 0.7045 (t0) cc_final: 0.5961 (t0) REVERT: A 278 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7951 (ttmm) REVERT: A 305 LYS cc_start: 0.7910 (mptp) cc_final: 0.7495 (mptp) REVERT: B 57 GLU cc_start: 0.7773 (tp30) cc_final: 0.7504 (tp30) REVERT: B 71 ASN cc_start: 0.8026 (p0) cc_final: 0.7786 (p0) REVERT: B 78 GLU cc_start: 0.7792 (tt0) cc_final: 0.7580 (tt0) REVERT: B 81 ASN cc_start: 0.8044 (t0) cc_final: 0.7779 (t0) REVERT: B 117 ASN cc_start: 0.8272 (m-40) cc_final: 0.8068 (m-40) REVERT: B 129 ASN cc_start: 0.8267 (m-40) cc_final: 0.8050 (t0) REVERT: C 5 VAL cc_start: 0.8626 (p) cc_final: 0.8379 (t) REVERT: C 15 THR cc_start: 0.8565 (m) cc_final: 0.8227 (p) REVERT: C 43 SER cc_start: 0.8490 (m) cc_final: 0.8145 (t) REVERT: C 47 LYS cc_start: 0.7005 (mttt) cc_final: 0.6622 (mtpt) REVERT: C 66 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8373 (mmtt) REVERT: C 94 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: C 111 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: C 112 GLU cc_start: 0.7325 (tt0) cc_final: 0.6996 (mt-10) REVERT: C 147 ASN cc_start: 0.8139 (m110) cc_final: 0.7745 (m110) REVERT: C 149 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7897 (tp) REVERT: C 154 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7817 (ttmm) REVERT: C 156 ASN cc_start: 0.8285 (p0) cc_final: 0.7936 (p0) REVERT: C 172 GLU cc_start: 0.6974 (pt0) cc_final: 0.6712 (pt0) REVERT: C 205 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8151 (mtmm) REVERT: C 229 TYR cc_start: 0.8449 (m-80) cc_final: 0.8205 (m-10) REVERT: C 257 LEU cc_start: 0.8289 (mp) cc_final: 0.7990 (mt) REVERT: C 266 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6289 (mtp) REVERT: C 305 LYS cc_start: 0.7711 (mptp) cc_final: 0.7474 (mptp) REVERT: D 52 VAL cc_start: 0.8449 (t) cc_final: 0.8166 (p) REVERT: D 53 ASN cc_start: 0.8344 (m-40) cc_final: 0.8015 (m-40) REVERT: D 139 GLU cc_start: 0.7303 (tt0) cc_final: 0.7052 (tt0) REVERT: D 140 PHE cc_start: 0.8187 (m-10) cc_final: 0.7986 (m-10) REVERT: D 147 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: E 23 ASN cc_start: 0.8023 (t0) cc_final: 0.7449 (t0) REVERT: E 62 LEU cc_start: 0.7511 (mt) cc_final: 0.6980 (mm) REVERT: E 65 PRO cc_start: 0.8680 (Cg_exo) cc_final: 0.8434 (Cg_endo) REVERT: E 75 SER cc_start: 0.8340 (m) cc_final: 0.7830 (p) REVERT: E 79 ILE cc_start: 0.8151 (mt) cc_final: 0.7944 (mt) REVERT: E 100 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6823 (mm-30) REVERT: E 102 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7445 (ttmm) REVERT: E 115 GLU cc_start: 0.6922 (tt0) cc_final: 0.6621 (tt0) REVERT: E 147 ASN cc_start: 0.8043 (m110) cc_final: 0.7309 (m110) REVERT: E 154 LYS cc_start: 0.8433 (tptt) cc_final: 0.8071 (tptt) REVERT: E 191 LEU cc_start: 0.8259 (mm) cc_final: 0.7784 (mp) REVERT: E 193 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7943 (mm-40) REVERT: E 198 TYR cc_start: 0.8636 (p90) cc_final: 0.8355 (p90) REVERT: E 199 VAL cc_start: 0.8343 (t) cc_final: 0.8046 (p) REVERT: E 205 LYS cc_start: 0.8423 (mttm) cc_final: 0.8083 (mtpm) REVERT: E 211 THR cc_start: 0.7982 (m) cc_final: 0.7478 (p) REVERT: E 234 LEU cc_start: 0.7874 (tp) cc_final: 0.7672 (mp) REVERT: E 277 THR cc_start: 0.8020 (m) cc_final: 0.7807 (t) REVERT: E 293 GLN cc_start: 0.7888 (pp30) cc_final: 0.7631 (pt0) REVERT: F 11 GLU cc_start: 0.7627 (pt0) cc_final: 0.7403 (pt0) REVERT: F 53 ASN cc_start: 0.8234 (m-40) cc_final: 0.7921 (m110) REVERT: F 81 ASN cc_start: 0.8152 (t0) cc_final: 0.7873 (t0) REVERT: F 116 LYS cc_start: 0.8610 (tmtm) cc_final: 0.8324 (tttm) REVERT: F 143 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7863 (tppp) outliers start: 88 outliers final: 62 residues processed: 482 average time/residue: 0.1242 time to fit residues: 81.9631 Evaluate side-chains 508 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 437 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 114 optimal weight: 0.0670 chunk 136 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN B 28 ASN C 45 ASN C 126 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 71 ASN E 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118935 restraints weight = 16669.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123723 restraints weight = 7978.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126883 restraints weight = 4668.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129046 restraints weight = 3065.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130557 restraints weight = 2169.652| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11583 Z= 0.126 Angle : 0.591 10.033 15708 Z= 0.306 Chirality : 0.042 0.165 1703 Planarity : 0.004 0.068 2022 Dihedral : 4.764 47.445 1559 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.81 % Allowed : 38.81 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1419 helix: 3.15 (0.28), residues: 339 sheet: 0.31 (0.37), residues: 216 loop : -1.54 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.020 0.002 TYR C 78 PHE 0.026 0.001 PHE B 140 TRP 0.010 0.001 TRP E 150 HIS 0.010 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00269 (11564) covalent geometry : angle 0.59031 (15669) SS BOND : bond 0.00275 ( 18) SS BOND : angle 0.76629 ( 36) hydrogen bonds : bond 0.04821 ( 437) hydrogen bonds : angle 4.24812 ( 1257) link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 0.90939 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 388 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8095 (mp) cc_final: 0.7865 (mt) REVERT: A 10 ASN cc_start: 0.8393 (p0) cc_final: 0.8138 (p0) REVERT: A 18 THR cc_start: 0.8189 (m) cc_final: 0.7490 (p) REVERT: A 60 TRP cc_start: 0.8407 (t60) cc_final: 0.8173 (t60) REVERT: A 84 ASN cc_start: 0.8058 (t0) cc_final: 0.7553 (t0) REVERT: A 111 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: A 123 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.7727 (m100) REVERT: A 157 SER cc_start: 0.8416 (t) cc_final: 0.7951 (p) REVERT: A 188 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: A 193 GLN cc_start: 0.7807 (tp40) cc_final: 0.7447 (tp40) REVERT: A 204 THR cc_start: 0.8216 (m) cc_final: 0.7709 (p) REVERT: A 205 LYS cc_start: 0.8682 (mttp) cc_final: 0.8428 (mttp) REVERT: A 211 THR cc_start: 0.8093 (m) cc_final: 0.7799 (t) REVERT: A 238 ASP cc_start: 0.6887 (t0) cc_final: 0.5674 (t0) REVERT: A 278 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7922 (ttmm) REVERT: A 305 LYS cc_start: 0.7676 (mptp) cc_final: 0.7298 (mptp) REVERT: B 57 GLU cc_start: 0.7750 (tp30) cc_final: 0.7477 (tp30) REVERT: B 81 ASN cc_start: 0.7947 (t0) cc_final: 0.7624 (t0) REVERT: C 15 THR cc_start: 0.8569 (m) cc_final: 0.8193 (p) REVERT: C 43 SER cc_start: 0.8329 (m) cc_final: 0.7861 (p) REVERT: C 66 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8338 (mmtt) REVERT: C 111 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: C 147 ASN cc_start: 0.8071 (m110) cc_final: 0.7634 (m110) REVERT: C 149 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7814 (tp) REVERT: C 154 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7978 (ttmm) REVERT: C 156 ASN cc_start: 0.8238 (p0) cc_final: 0.7847 (p0) REVERT: C 172 GLU cc_start: 0.6984 (pt0) cc_final: 0.6703 (pt0) REVERT: C 205 LYS cc_start: 0.8290 (mtmm) cc_final: 0.8078 (mtmm) REVERT: C 229 TYR cc_start: 0.8356 (m-80) cc_final: 0.8033 (m-10) REVERT: C 257 LEU cc_start: 0.8247 (mp) cc_final: 0.7975 (mt) REVERT: C 266 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5934 (mtp) REVERT: C 305 LYS cc_start: 0.7551 (mptp) cc_final: 0.7290 (mptp) REVERT: D 27 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6399 (ttm110) REVERT: D 53 ASN cc_start: 0.8355 (m-40) cc_final: 0.8051 (m-40) REVERT: D 147 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: E 23 ASN cc_start: 0.7986 (t0) cc_final: 0.7426 (t0) REVERT: E 62 LEU cc_start: 0.7398 (mt) cc_final: 0.6860 (mm) REVERT: E 75 SER cc_start: 0.8304 (m) cc_final: 0.7964 (p) REVERT: E 100 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6715 (mm-30) REVERT: E 115 GLU cc_start: 0.6817 (tt0) cc_final: 0.6465 (tt0) REVERT: E 147 ASN cc_start: 0.7899 (m110) cc_final: 0.7302 (m110) REVERT: E 154 LYS cc_start: 0.8406 (tptt) cc_final: 0.8027 (tptt) REVERT: E 191 LEU cc_start: 0.8200 (mm) cc_final: 0.7925 (mp) REVERT: E 197 THR cc_start: 0.8471 (p) cc_final: 0.7921 (t) REVERT: E 198 TYR cc_start: 0.8652 (p90) cc_final: 0.8262 (p90) REVERT: E 201 VAL cc_start: 0.8159 (t) cc_final: 0.7669 (p) REVERT: E 205 LYS cc_start: 0.8288 (mttm) cc_final: 0.7947 (mtpm) REVERT: E 211 THR cc_start: 0.7809 (m) cc_final: 0.7292 (p) REVERT: E 293 GLN cc_start: 0.7809 (pp30) cc_final: 0.7566 (pt0) REVERT: E 305 LYS cc_start: 0.7733 (mptt) cc_final: 0.7467 (mptt) REVERT: F 11 GLU cc_start: 0.7544 (pt0) cc_final: 0.7322 (pt0) REVERT: F 81 ASN cc_start: 0.7911 (t0) cc_final: 0.7623 (t0) REVERT: F 105 GLU cc_start: 0.7044 (tp30) cc_final: 0.6285 (tp30) REVERT: F 143 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7850 (tppp) outliers start: 60 outliers final: 42 residues processed: 417 average time/residue: 0.1221 time to fit residues: 69.9938 Evaluate side-chains 440 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 389 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117932 restraints weight = 16784.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122681 restraints weight = 8043.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125842 restraints weight = 4709.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127996 restraints weight = 3098.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129502 restraints weight = 2198.780| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11583 Z= 0.210 Angle : 0.627 9.431 15708 Z= 0.327 Chirality : 0.043 0.175 1703 Planarity : 0.004 0.066 2022 Dihedral : 4.782 46.460 1559 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.81 % Allowed : 37.93 % Favored : 57.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.22), residues: 1419 helix: 2.94 (0.28), residues: 339 sheet: 0.23 (0.35), residues: 246 loop : -1.65 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.027 0.002 TYR E 145 PHE 0.024 0.002 PHE D 140 TRP 0.014 0.001 TRP C 177 HIS 0.010 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00451 (11564) covalent geometry : angle 0.62552 (15669) SS BOND : bond 0.00398 ( 18) SS BOND : angle 0.98437 ( 36) hydrogen bonds : bond 0.05578 ( 437) hydrogen bonds : angle 4.40974 ( 1257) link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 1.45652 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 404 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8081 (mp) cc_final: 0.7785 (mt) REVERT: A 18 THR cc_start: 0.8223 (m) cc_final: 0.7570 (p) REVERT: A 84 ASN cc_start: 0.8115 (t0) cc_final: 0.7581 (t0) REVERT: A 111 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: A 123 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7693 (m100) REVERT: A 157 SER cc_start: 0.8453 (t) cc_final: 0.8008 (p) REVERT: A 177 TRP cc_start: 0.8574 (p90) cc_final: 0.8345 (p90) REVERT: A 188 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 193 GLN cc_start: 0.7827 (tp40) cc_final: 0.7514 (tp40) REVERT: A 204 THR cc_start: 0.8214 (m) cc_final: 0.7731 (p) REVERT: A 205 LYS cc_start: 0.8711 (mttp) cc_final: 0.8475 (mttp) REVERT: A 211 THR cc_start: 0.8146 (m) cc_final: 0.7843 (t) REVERT: A 238 ASP cc_start: 0.6860 (t0) cc_final: 0.5632 (t0) REVERT: A 278 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7930 (ttmm) REVERT: A 305 LYS cc_start: 0.7797 (mptp) cc_final: 0.7429 (mptp) REVERT: B 57 GLU cc_start: 0.7746 (tp30) cc_final: 0.7473 (tp30) REVERT: B 71 ASN cc_start: 0.7975 (p0) cc_final: 0.7686 (p0) REVERT: B 81 ASN cc_start: 0.7973 (t0) cc_final: 0.7653 (t0) REVERT: B 140 PHE cc_start: 0.8031 (m-10) cc_final: 0.7805 (m-10) REVERT: B 153 LYS cc_start: 0.8635 (mttt) cc_final: 0.8388 (mptt) REVERT: C 15 THR cc_start: 0.8567 (m) cc_final: 0.8157 (p) REVERT: C 43 SER cc_start: 0.8373 (m) cc_final: 0.7980 (p) REVERT: C 66 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8344 (mmtt) REVERT: C 111 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8103 (m-10) REVERT: C 147 ASN cc_start: 0.8122 (m110) cc_final: 0.7699 (m110) REVERT: C 149 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7867 (tp) REVERT: C 154 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7843 (ttmm) REVERT: C 156 ASN cc_start: 0.8205 (p0) cc_final: 0.7796 (p0) REVERT: C 172 GLU cc_start: 0.6946 (pt0) cc_final: 0.6676 (pt0) REVERT: C 205 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8122 (mtmm) REVERT: C 229 TYR cc_start: 0.8377 (m-80) cc_final: 0.8055 (m-10) REVERT: C 245 THR cc_start: 0.8400 (p) cc_final: 0.8172 (t) REVERT: C 257 LEU cc_start: 0.8275 (mp) cc_final: 0.7990 (mt) REVERT: C 266 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.6091 (mtp) REVERT: C 305 LYS cc_start: 0.7642 (mptp) cc_final: 0.7358 (mptp) REVERT: D 27 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6381 (ttm110) REVERT: D 52 VAL cc_start: 0.8405 (t) cc_final: 0.8101 (p) REVERT: D 53 ASN cc_start: 0.8324 (m-40) cc_final: 0.8021 (m-40) REVERT: D 77 MET cc_start: 0.6837 (mmt) cc_final: 0.6597 (mmt) REVERT: D 147 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: E 23 ASN cc_start: 0.8007 (t0) cc_final: 0.7432 (t0) REVERT: E 62 LEU cc_start: 0.7412 (mt) cc_final: 0.6826 (mm) REVERT: E 65 PRO cc_start: 0.8687 (Cg_exo) cc_final: 0.8467 (Cg_endo) REVERT: E 75 SER cc_start: 0.8287 (m) cc_final: 0.7941 (p) REVERT: E 100 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6716 (mm-30) REVERT: E 102 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7539 (mtmt) REVERT: E 115 GLU cc_start: 0.6808 (tt0) cc_final: 0.6480 (tt0) REVERT: E 143 SER cc_start: 0.7722 (t) cc_final: 0.7423 (m) REVERT: E 147 ASN cc_start: 0.8015 (m110) cc_final: 0.7334 (m110) REVERT: E 154 LYS cc_start: 0.8418 (tptt) cc_final: 0.8032 (tptt) REVERT: E 191 LEU cc_start: 0.8185 (mm) cc_final: 0.7915 (mp) REVERT: E 197 THR cc_start: 0.8438 (p) cc_final: 0.7865 (t) REVERT: E 198 TYR cc_start: 0.8642 (p90) cc_final: 0.8227 (p90) REVERT: E 201 VAL cc_start: 0.8220 (t) cc_final: 0.7776 (p) REVERT: E 205 LYS cc_start: 0.8333 (mttm) cc_final: 0.7977 (mtpm) REVERT: E 211 THR cc_start: 0.7852 (m) cc_final: 0.7322 (p) REVERT: E 293 GLN cc_start: 0.7836 (pp30) cc_final: 0.7601 (pt0) REVERT: E 305 LYS cc_start: 0.7787 (mptt) cc_final: 0.7511 (mptt) REVERT: F 81 ASN cc_start: 0.7936 (t0) cc_final: 0.7662 (t0) REVERT: F 143 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7817 (tppp) outliers start: 60 outliers final: 46 residues processed: 433 average time/residue: 0.1257 time to fit residues: 74.2829 Evaluate side-chains 459 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 404 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118620 restraints weight = 16838.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123347 restraints weight = 8074.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126473 restraints weight = 4730.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128650 restraints weight = 3118.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130167 restraints weight = 2199.810| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11583 Z= 0.180 Angle : 0.606 9.416 15708 Z= 0.316 Chirality : 0.043 0.163 1703 Planarity : 0.004 0.061 2022 Dihedral : 4.683 47.852 1559 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.89 % Allowed : 38.57 % Favored : 56.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1419 helix: 3.00 (0.28), residues: 339 sheet: 0.17 (0.34), residues: 246 loop : -1.60 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.026 0.002 TYR E 145 PHE 0.021 0.002 PHE E 111 TRP 0.011 0.001 TRP C 177 HIS 0.010 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00389 (11564) covalent geometry : angle 0.60464 (15669) SS BOND : bond 0.00324 ( 18) SS BOND : angle 0.88733 ( 36) hydrogen bonds : bond 0.05217 ( 437) hydrogen bonds : angle 4.30213 ( 1257) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.11496 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.43 seconds wall clock time: 38 minutes 42.02 seconds (2322.02 seconds total)