Starting phenix.real_space_refine on Tue Nov 18 12:14:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itn_60872/11_2025/9itn_60872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itn_60872/11_2025/9itn_60872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9itn_60872/11_2025/9itn_60872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itn_60872/11_2025/9itn_60872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itn_60872/11_2025/9itn_60872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itn_60872/11_2025/9itn_60872.map" } resolution = 3.48 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= -0.000 sd= 0.011 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 39 5.16 5 C 9206 2.51 5 N 2394 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14103 Number of models: 1 Model: "" Number of chains: 16 Chain: "Y" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1215 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 1, 'TRANS': 150} Chain: "V" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "X" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1198 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 148} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1235 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 506 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "T" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2064 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2038 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 3.48, per 1000 atoms: 0.25 Number of scatterers: 14103 At special positions: 0 Unit cell: (93.93, 146.01, 225.06, 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 39 16.00 O 2464 8.00 N 2394 7.00 C 9206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 173 " distance=2.82 Simple disulfide: pdb=" SG CYS Z 135 " - pdb=" SG CYS Z 173 " distance=2.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 709.6 milliseconds 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 84.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'Y' and resid 9 through 29 removed outlier: 4.037A pdb=" N ALA Y 13 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 142 removed outlier: 3.513A pdb=" N ALA Y 142 " --> pdb=" O ARG Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 159 Processing helix chain 'V' and resid 7 through 26 Processing helix chain 'V' and resid 30 through 80 removed outlier: 3.717A pdb=" N GLU V 52 " --> pdb=" O VAL V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 111 Processing helix chain 'V' and resid 112 through 117 Processing helix chain 'V' and resid 119 through 125 removed outlier: 3.580A pdb=" N SER V 122 " --> pdb=" O ARG V 119 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA V 124 " --> pdb=" O LEU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 137 removed outlier: 3.553A pdb=" N THR V 135 " --> pdb=" O LEU V 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 60 removed outlier: 4.158A pdb=" N ALA X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Proline residue: X 32 - end of helix removed outlier: 4.170A pdb=" N ALA X 51 " --> pdb=" O SER X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 143 removed outlier: 4.042A pdb=" N GLU X 66 " --> pdb=" O ARG X 62 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU X 143 " --> pdb=" O VAL X 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 119 Proline residue: U 32 - end of helix removed outlier: 4.160A pdb=" N ARG U 119 " --> pdb=" O GLN U 115 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 137 Processing helix chain 'U' and resid 150 through 159 Processing helix chain 'H' and resid 3 through 38 removed outlier: 4.481A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 71 removed outlier: 4.025A pdb=" N ALA H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 38 Proline residue: I 20 - end of helix Processing helix chain 'I' and resid 41 through 72 removed outlier: 4.469A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA I 58 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 3.614A pdb=" N VAL J 7 " --> pdb=" O GLY J 3 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 71 removed outlier: 3.757A pdb=" N VAL J 45 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA J 58 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 17 removed outlier: 3.874A pdb=" N GLY K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 38 removed outlier: 4.154A pdb=" N VAL K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY K 23 " --> pdb=" O GLY K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 66 removed outlier: 3.909A pdb=" N ALA K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 71 Processing helix chain 'L' and resid 3 through 16 removed outlier: 3.693A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 37 removed outlier: 3.519A pdb=" N ARG L 37 " --> pdb=" O GLN L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 41 through 71 removed outlier: 3.808A pdb=" N TYR L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.859A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU M 57 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA M 58 " --> pdb=" O ALA M 54 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 38 removed outlier: 4.136A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Proline residue: N 20 - end of helix Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.521A pdb=" N GLU N 57 " --> pdb=" O ILE N 53 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA N 60 " --> pdb=" O THR N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 38 Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 41 through 72 removed outlier: 5.202A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 38 removed outlier: 3.593A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) Proline residue: P 20 - end of helix Processing helix chain 'P' and resid 41 through 72 removed outlier: 4.742A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.699A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 41 through 72 removed outlier: 4.701A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 71 removed outlier: 3.834A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE T 56 " --> pdb=" O PHE T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 4.002A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.748A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 178 removed outlier: 3.703A pdb=" N GLY T 177 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 Processing helix chain 'T' and resid 192 through 211 Processing helix chain 'T' and resid 215 through 221 removed outlier: 3.803A pdb=" N LYS T 219 " --> pdb=" O PRO T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 268 removed outlier: 3.755A pdb=" N VAL T 231 " --> pdb=" O ILE T 227 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.657A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 21 removed outlier: 3.637A pdb=" N ALA Z 20 " --> pdb=" O ILE Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 70 removed outlier: 3.656A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.671A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU Z 88 " --> pdb=" O MET Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 124 Proline residue: Z 108 - end of helix removed outlier: 3.739A pdb=" N GLY Z 124 " --> pdb=" O GLY Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 176 Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.726A pdb=" N ALA Z 196 " --> pdb=" O ASN Z 192 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA Z 212 " --> pdb=" O TRP Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 220 removed outlier: 3.938A pdb=" N LYS Z 219 " --> pdb=" O PRO Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 225 removed outlier: 3.987A pdb=" N ASN Z 225 " --> pdb=" O PHE Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 268 removed outlier: 4.282A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 3.704A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.825A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 39 through 41 removed outlier: 7.587A pdb=" N ILE Z 48 " --> pdb=" O PHE Z 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 133 through 135 1238 hydrogen bonds defined for protein. 3684 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: 2.45 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4644 1.34 - 1.46: 2848 1.46 - 1.58: 6755 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 14321 Sorted by residual: bond pdb=" N ILE O 70 " pdb=" CA ILE O 70 " ideal model delta sigma weight residual 1.460 1.496 -0.035 1.19e-02 7.06e+03 8.88e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.56e+00 bond pdb=" N ILE P 66 " pdb=" CA ILE P 66 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.82e+00 bond pdb=" N ILE P 70 " pdb=" CA ILE P 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.71e+00 bond pdb=" N VAL P 65 " pdb=" CA VAL P 65 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.54e+00 ... (remaining 14316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 18748 2.08 - 4.15: 519 4.15 - 6.23: 93 6.23 - 8.31: 25 8.31 - 10.38: 10 Bond angle restraints: 19395 Sorted by residual: angle pdb=" N LEU X 121 " pdb=" CA LEU X 121 " pdb=" C LEU X 121 " ideal model delta sigma weight residual 111.14 105.97 5.17 1.08e+00 8.57e-01 2.29e+01 angle pdb=" CA LYS X 78 " pdb=" CB LYS X 78 " pdb=" CG LYS X 78 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.97e+01 angle pdb=" N ARG V 86 " pdb=" CA ARG V 86 " pdb=" C ARG V 86 " ideal model delta sigma weight residual 113.01 107.99 5.02 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA GLN Z 74 " pdb=" CB GLN Z 74 " pdb=" CG GLN Z 74 " ideal model delta sigma weight residual 114.10 122.36 -8.26 2.00e+00 2.50e-01 1.70e+01 angle pdb=" N ILE M 70 " pdb=" CA ILE M 70 " pdb=" C ILE M 70 " ideal model delta sigma weight residual 113.42 108.65 4.77 1.17e+00 7.31e-01 1.67e+01 ... (remaining 19390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7172 17.93 - 35.87: 997 35.87 - 53.80: 266 53.80 - 71.73: 40 71.73 - 89.67: 25 Dihedral angle restraints: 8500 sinusoidal: 3253 harmonic: 5247 Sorted by residual: dihedral pdb=" CA MET U 34 " pdb=" C MET U 34 " pdb=" N ASN U 35 " pdb=" CA ASN U 35 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CB CYS T 135 " pdb=" SG CYS T 135 " pdb=" SG CYS T 173 " pdb=" CB CYS T 173 " ideal model delta sinusoidal sigma weight residual 93.00 50.84 42.16 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CA PHE T 52 " pdb=" C PHE T 52 " pdb=" N VAL T 53 " pdb=" CA VAL T 53 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 8497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1748 0.051 - 0.103: 475 0.103 - 0.154: 91 0.154 - 0.205: 15 0.205 - 0.257: 5 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CB VAL U 80 " pdb=" CA VAL U 80 " pdb=" CG1 VAL U 80 " pdb=" CG2 VAL U 80 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE T 200 " pdb=" CA ILE T 200 " pdb=" CG1 ILE T 200 " pdb=" CG2 ILE T 200 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE H 18 " pdb=" CA ILE H 18 " pdb=" CG1 ILE H 18 " pdb=" CG2 ILE H 18 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2331 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO Q 20 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 19 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO H 20 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO H 20 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 20 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY M 19 " -0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO M 20 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 20 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 20 " -0.038 5.00e-02 4.00e+02 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1908 2.75 - 3.29: 15826 3.29 - 3.83: 24977 3.83 - 4.36: 27238 4.36 - 4.90: 45940 Nonbonded interactions: 115889 Sorted by model distance: nonbonded pdb=" O ALA X 72 " pdb=" NH1 ARG U 71 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASN N 43 " pdb=" N ARG N 44 " model vdw 2.242 3.120 nonbonded pdb=" O ALA U 129 " pdb=" OG1 THR U 133 " model vdw 2.244 3.040 nonbonded pdb=" ND2 ASN V 17 " pdb=" OD2 ASP Z 59 " model vdw 2.270 3.120 nonbonded pdb=" O PHE T 86 " pdb=" OG SER T 90 " model vdw 2.292 3.040 ... (remaining 115884 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 'H' selection = (chain 'I' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'K' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'M' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'N' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'O' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'P' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'Q' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) } ncs_group { reference = (chain 'T' and (resid 19 through 136 or resid 169 through 304)) selection = (chain 'Z' and resid 19 through 304) } ncs_group { reference = (chain 'U' and (resid 8 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 157)) selection = (chain 'V' and (resid 8 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 157)) selection = chain 'X' selection = (chain 'Y' and (resid 8 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.360 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.011 0.958 14323 Z= 0.572 Angle : 0.911 48.454 19399 Z= 0.495 Chirality : 0.049 0.257 2334 Planarity : 0.007 0.086 2483 Dihedral : 18.093 89.665 5118 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 0.78 % Allowed : 37.59 % Favored : 61.63 % 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: -0.27 (0.19), residues: 1822 helix: 0.32 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Y 119 TYR 0.031 0.002 TYR U 65 PHE 0.041 0.002 PHE Z 123 TRP 0.031 0.004 TRP T 122 HIS 0.011 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00474 (14321) covalent geometry : angle 0.83329 (19395) SS BOND : bond 0.87643 ( 2) SS BOND : angle 25.57229 ( 4) hydrogen bonds : bond 0.13403 ( 1238) hydrogen bonds : angle 5.93637 ( 3684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 327 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9125 (mm-30) REVERT: U 108 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8742 (mp0) REVERT: T 122 TRP cc_start: 0.9269 (m-10) cc_final: 0.9028 (m-10) REVERT: Z 33 GLU cc_start: 0.7905 (mp0) cc_final: 0.7534 (mp0) REVERT: Z 85 GLU cc_start: 0.9110 (tt0) cc_final: 0.8871 (tt0) REVERT: Z 101 LYS cc_start: 0.8789 (pttm) cc_final: 0.8580 (pttp) outliers start: 11 outliers final: 7 residues processed: 332 average time/residue: 0.1124 time to fit residues: 56.3228 Evaluate side-chains 310 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 303 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain Z residue 74 GLN Chi-restraints excluded: chain Z residue 112 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 GLN Q 33 GLN ** Z 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.097851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076168 restraints weight = 48195.615| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.70 r_work: 0.3309 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14323 Z= 0.157 Angle : 0.604 8.470 19399 Z= 0.323 Chirality : 0.041 0.185 2334 Planarity : 0.005 0.085 2483 Dihedral : 4.835 50.441 1998 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.18 % Allowed : 30.71 % Favored : 64.11 % 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: 0.71 (0.19), residues: 1822 helix: 1.09 (0.13), residues: 1461 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 71 TYR 0.028 0.002 TYR N 48 PHE 0.028 0.001 PHE Z 123 TRP 0.011 0.002 TRP T 208 HIS 0.008 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00324 (14321) covalent geometry : angle 0.60223 (19395) SS BOND : bond 0.01453 ( 2) SS BOND : angle 3.01658 ( 4) hydrogen bonds : bond 0.05320 ( 1238) hydrogen bonds : angle 4.20463 ( 3684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 349 time to evaluate : 0.551 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: Y 119 ARG cc_start: 0.8813 (tmm160) cc_final: 0.8581 (ttp80) REVERT: V 79 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8341 (mm) REVERT: V 130 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7618 (p0) REVERT: X 18 PHE cc_start: 0.9269 (t80) cc_final: 0.8902 (t80) REVERT: X 85 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9096 (mm-30) REVERT: U 34 MET cc_start: 0.8574 (pmm) cc_final: 0.8324 (pmm) REVERT: U 117 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6489 (ttp80) REVERT: I 57 GLU cc_start: 0.9386 (tp30) cc_final: 0.9155 (tp30) REVERT: M 57 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8671 (mm-30) REVERT: T 85 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: T 122 TRP cc_start: 0.9251 (m-10) cc_final: 0.8943 (m-10) REVERT: Z 33 GLU cc_start: 0.7884 (mp0) cc_final: 0.7528 (mp0) REVERT: Z 74 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: Z 85 GLU cc_start: 0.9149 (tt0) cc_final: 0.8901 (tt0) REVERT: Z 92 TYR cc_start: 0.9296 (t80) cc_final: 0.8931 (t80) REVERT: Z 206 GLU cc_start: 0.9214 (mm-30) cc_final: 0.9005 (mm-30) outliers start: 73 outliers final: 39 residues processed: 389 average time/residue: 0.1118 time to fit residues: 65.4914 Evaluate side-chains 352 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 118 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain U residue 30 TYR Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 74 GLN Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 77 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 171 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN U 84 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.097345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076117 restraints weight = 48501.293| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.72 r_work: 0.3307 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14323 Z= 0.148 Angle : 0.591 7.962 19399 Z= 0.312 Chirality : 0.041 0.196 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.480 52.362 1992 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.38 % Allowed : 30.99 % Favored : 62.62 % 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: 0.92 (0.19), residues: 1822 helix: 1.25 (0.13), residues: 1461 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 249 TYR 0.026 0.002 TYR N 48 PHE 0.019 0.001 PHE L 62 TRP 0.009 0.001 TRP T 208 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00311 (14321) covalent geometry : angle 0.59077 (19395) SS BOND : bond 0.00133 ( 2) SS BOND : angle 1.37884 ( 4) hydrogen bonds : bond 0.05003 ( 1238) hydrogen bonds : angle 3.99141 ( 3684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 329 time to evaluate : 0.566 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: Y 90 GLN cc_start: 0.8872 (mt0) cc_final: 0.8669 (mt0) REVERT: V 79 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8369 (mm) REVERT: V 130 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7528 (p0) REVERT: V 131 LEU cc_start: 0.8663 (mt) cc_final: 0.8253 (pp) REVERT: X 18 PHE cc_start: 0.9291 (t80) cc_final: 0.8928 (t80) REVERT: X 115 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8785 (tm-30) REVERT: U 23 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6709 (t80) REVERT: U 34 MET cc_start: 0.8681 (pmm) cc_final: 0.8399 (pmm) REVERT: U 103 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8750 (pp20) REVERT: U 117 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6947 (ttp80) REVERT: I 57 GLU cc_start: 0.9406 (tp30) cc_final: 0.9151 (tp30) REVERT: J 61 ILE cc_start: 0.9202 (mm) cc_final: 0.8909 (pt) REVERT: L 33 GLN cc_start: 0.9260 (mt0) cc_final: 0.8972 (mm-40) REVERT: M 41 ILE cc_start: 0.8612 (tp) cc_final: 0.8348 (tt) REVERT: Q 37 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8418 (mpt-90) REVERT: T 122 TRP cc_start: 0.9308 (m-10) cc_final: 0.9000 (m-10) REVERT: T 294 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9336 (mm) REVERT: Z 85 GLU cc_start: 0.9161 (tt0) cc_final: 0.8863 (tt0) REVERT: Z 92 TYR cc_start: 0.9288 (t80) cc_final: 0.8909 (t80) REVERT: Z 206 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9020 (mm-30) REVERT: Z 267 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8168 (mm) REVERT: Z 280 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 90 outliers final: 55 residues processed: 380 average time/residue: 0.1147 time to fit residues: 65.1208 Evaluate side-chains 368 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 86 ARG Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 118 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain U residue 30 TYR Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 267 LEU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 82 optimal weight: 0.0980 chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.097395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076125 restraints weight = 48232.252| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.78 r_work: 0.3294 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14323 Z= 0.146 Angle : 0.591 8.629 19399 Z= 0.312 Chirality : 0.041 0.199 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.279 51.000 1989 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.31 % Allowed : 30.43 % Favored : 63.26 % 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: 0.97 (0.19), residues: 1822 helix: 1.30 (0.13), residues: 1466 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 71 TYR 0.022 0.002 TYR N 48 PHE 0.018 0.001 PHE L 62 TRP 0.008 0.001 TRP T 208 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00308 (14321) covalent geometry : angle 0.59074 (19395) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.90596 ( 4) hydrogen bonds : bond 0.04871 ( 1238) hydrogen bonds : angle 3.91810 ( 3684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 327 time to evaluate : 0.561 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: V 79 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8361 (mm) REVERT: V 130 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7511 (p0) REVERT: V 131 LEU cc_start: 0.8644 (mt) cc_final: 0.8253 (pp) REVERT: X 18 PHE cc_start: 0.9321 (t80) cc_final: 0.8916 (t80) REVERT: X 115 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8736 (tm-30) REVERT: U 23 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6730 (t80) REVERT: U 34 MET cc_start: 0.8692 (pmm) cc_final: 0.8408 (pmm) REVERT: U 103 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8748 (pp20) REVERT: U 117 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6946 (ttp80) REVERT: I 57 GLU cc_start: 0.9395 (tp30) cc_final: 0.9173 (tp30) REVERT: L 33 GLN cc_start: 0.9267 (mt0) cc_final: 0.8913 (mm110) REVERT: M 37 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7651 (ttm-80) REVERT: M 41 ILE cc_start: 0.8635 (tp) cc_final: 0.8322 (tt) REVERT: O 1 MET cc_start: 0.6553 (tpt) cc_final: 0.6151 (tpt) REVERT: O 49 MET cc_start: 0.9138 (tmm) cc_final: 0.8690 (tmm) REVERT: P 42 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7980 (pp20) REVERT: T 85 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: T 122 TRP cc_start: 0.9312 (m-10) cc_final: 0.9043 (m-10) REVERT: T 294 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9327 (mm) REVERT: Z 85 GLU cc_start: 0.9159 (tt0) cc_final: 0.8826 (tt0) REVERT: Z 92 TYR cc_start: 0.9249 (t80) cc_final: 0.8947 (t80) REVERT: Z 267 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (mm) REVERT: Z 280 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8561 (tm-30) outliers start: 89 outliers final: 63 residues processed: 379 average time/residue: 0.1157 time to fit residues: 65.7360 Evaluate side-chains 377 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 304 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 86 ARG Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 118 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 74 GLN Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain U residue 30 TYR Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 267 LEU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 ASN Q 33 GLN ** Z 121 ASN ** 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 = 0.3831 r_free = 0.3831 target = 0.093296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071840 restraints weight = 48910.377| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.56 r_work: 0.3202 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14323 Z= 0.254 Angle : 0.688 9.447 19399 Z= 0.363 Chirality : 0.044 0.259 2334 Planarity : 0.006 0.085 2483 Dihedral : 4.410 50.651 1989 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 8.44 % Allowed : 31.13 % Favored : 60.43 % 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: 0.87 (0.19), residues: 1822 helix: 1.21 (0.13), residues: 1453 sheet: None (None), residues: 0 loop : -1.92 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 86 TYR 0.024 0.002 TYR N 48 PHE 0.026 0.002 PHE L 62 TRP 0.009 0.002 TRP Z 208 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00558 (14321) covalent geometry : angle 0.68787 (19395) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.88862 ( 4) hydrogen bonds : bond 0.05432 ( 1238) hydrogen bonds : angle 4.07742 ( 3684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 306 time to evaluate : 0.502 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: symmetry clash revert: symmetry clash REVERT: Y 90 GLN cc_start: 0.8941 (mt0) cc_final: 0.8617 (mt0) REVERT: V 34 MET cc_start: 0.8471 (mmt) cc_final: 0.8261 (mmm) REVERT: V 46 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: V 79 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8390 (mm) REVERT: X 18 PHE cc_start: 0.9368 (t80) cc_final: 0.8993 (t80) REVERT: X 74 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8812 (tm-30) REVERT: X 78 LYS cc_start: 0.7985 (pttm) cc_final: 0.7668 (pttm) REVERT: X 106 LYS cc_start: 0.9334 (ptpp) cc_final: 0.9128 (ptpp) REVERT: X 115 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8757 (tm-30) REVERT: U 23 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6339 (t80) REVERT: U 117 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6782 (ttp80) REVERT: L 33 GLN cc_start: 0.9256 (mt0) cc_final: 0.8905 (mm110) REVERT: M 41 ILE cc_start: 0.8745 (tp) cc_final: 0.8464 (tt) REVERT: O 1 MET cc_start: 0.7065 (tpt) cc_final: 0.6728 (tpt) REVERT: O 49 MET cc_start: 0.9214 (tmm) cc_final: 0.8819 (tmm) REVERT: P 42 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8075 (pp20) REVERT: T 85 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: T 122 TRP cc_start: 0.9297 (m-10) cc_final: 0.9021 (m-10) REVERT: Z 92 TYR cc_start: 0.9249 (t80) cc_final: 0.8891 (t80) REVERT: Z 280 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8366 (tm-30) outliers start: 119 outliers final: 81 residues processed: 373 average time/residue: 0.1097 time to fit residues: 61.6006 Evaluate side-chains 369 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 281 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 118 ILE Chi-restraints excluded: chain V residue 127 GLN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 11 PHE Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 74 GLN Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 63 ARG Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 264 MET Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 272 LEU Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN ** Z 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.095375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074126 restraints weight = 47893.376| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.64 r_work: 0.3253 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14323 Z= 0.153 Angle : 0.631 11.061 19399 Z= 0.326 Chirality : 0.042 0.316 2334 Planarity : 0.005 0.086 2483 Dihedral : 4.390 51.755 1989 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.88 % Allowed : 32.55 % Favored : 60.57 % 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: 1.10 (0.19), residues: 1822 helix: 1.36 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 86 TYR 0.020 0.002 TYR N 48 PHE 0.022 0.001 PHE L 62 TRP 0.009 0.001 TRP Z 208 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00326 (14321) covalent geometry : angle 0.63104 (19395) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.73129 ( 4) hydrogen bonds : bond 0.05030 ( 1238) hydrogen bonds : angle 3.93205 ( 3684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 303 time to evaluate : 0.564 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: symmetry clash revert: symmetry clash REVERT: Y 119 ARG cc_start: 0.8778 (tmm160) cc_final: 0.8562 (ttp80) REVERT: V 79 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8323 (mm) REVERT: V 131 LEU cc_start: 0.8622 (mt) cc_final: 0.8264 (pp) REVERT: X 18 PHE cc_start: 0.9343 (t80) cc_final: 0.8894 (t80) REVERT: X 74 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8825 (tm-30) REVERT: X 78 LYS cc_start: 0.7982 (pttm) cc_final: 0.7732 (pttm) REVERT: X 106 LYS cc_start: 0.9352 (ptpp) cc_final: 0.9139 (ptpp) REVERT: X 115 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8744 (tm-30) REVERT: U 23 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6508 (t80) REVERT: U 117 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6983 (ttp80) REVERT: K 1 MET cc_start: 0.8114 (tpt) cc_final: 0.7786 (tpp) REVERT: L 33 GLN cc_start: 0.9287 (mt0) cc_final: 0.8914 (mm110) REVERT: M 41 ILE cc_start: 0.8680 (tp) cc_final: 0.8339 (tt) REVERT: M 70 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8543 (mp) REVERT: O 1 MET cc_start: 0.7025 (tpt) cc_final: 0.6693 (tpt) REVERT: O 49 MET cc_start: 0.9178 (tmm) cc_final: 0.8745 (tmm) REVERT: P 42 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7986 (pp20) REVERT: T 85 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: T 122 TRP cc_start: 0.9335 (m-10) cc_final: 0.9048 (m-10) REVERT: Z 33 GLU cc_start: 0.8129 (mp0) cc_final: 0.7855 (mp0) REVERT: Z 125 LEU cc_start: 0.9208 (mp) cc_final: 0.8988 (mp) REVERT: Z 195 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.9150 (t80) REVERT: Z 277 TYR cc_start: 0.9242 (m-80) cc_final: 0.8604 (m-80) REVERT: Z 280 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8569 (tm-30) outliers start: 97 outliers final: 71 residues processed: 359 average time/residue: 0.1189 time to fit residues: 63.5849 Evaluate side-chains 368 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 289 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 127 GLN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 74 GLN Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 63 ARG Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 65 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 153 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 137 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075896 restraints weight = 48142.727| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.71 r_work: 0.3292 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14323 Z= 0.141 Angle : 0.631 11.167 19399 Z= 0.325 Chirality : 0.042 0.281 2334 Planarity : 0.005 0.084 2483 Dihedral : 4.318 51.817 1989 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.17 % Allowed : 33.48 % Favored : 60.35 % 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: 1.20 (0.19), residues: 1822 helix: 1.45 (0.13), residues: 1469 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 86 TYR 0.017 0.002 TYR N 48 PHE 0.020 0.001 PHE L 62 TRP 0.011 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00295 (14321) covalent geometry : angle 0.63099 (19395) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.68580 ( 4) hydrogen bonds : bond 0.04774 ( 1238) hydrogen bonds : angle 3.82695 ( 3684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 310 time to evaluate : 0.570 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 84 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8925 (mm-40) REVERT: V 79 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8350 (mm) REVERT: X 18 PHE cc_start: 0.9346 (t80) cc_final: 0.8916 (t80) REVERT: X 74 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: X 78 LYS cc_start: 0.7997 (pttm) cc_final: 0.7739 (pttm) REVERT: X 115 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8717 (tm-30) REVERT: U 97 GLN cc_start: 0.8235 (mp10) cc_final: 0.8028 (mp10) REVERT: K 1 MET cc_start: 0.8133 (tpt) cc_final: 0.7578 (tpp) REVERT: L 33 GLN cc_start: 0.9303 (mt0) cc_final: 0.8942 (mm110) REVERT: M 41 ILE cc_start: 0.8652 (tp) cc_final: 0.8294 (tt) REVERT: M 70 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8494 (mp) REVERT: O 1 MET cc_start: 0.6721 (tpt) cc_final: 0.6512 (tpt) REVERT: O 49 MET cc_start: 0.9161 (tmm) cc_final: 0.8854 (tmm) REVERT: P 42 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: T 85 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: T 122 TRP cc_start: 0.9260 (m-10) cc_final: 0.8987 (m-10) REVERT: Z 92 TYR cc_start: 0.9248 (t80) cc_final: 0.8902 (t80) REVERT: Z 195 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9113 (t80) REVERT: Z 277 TYR cc_start: 0.9210 (m-80) cc_final: 0.8665 (m-80) REVERT: Z 280 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8610 (tm-30) outliers start: 87 outliers final: 67 residues processed: 363 average time/residue: 0.1141 time to fit residues: 62.2587 Evaluate side-chains 371 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 297 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 74 GLN Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 63 ARG Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.095732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074551 restraints weight = 47955.881| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.66 r_work: 0.3266 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14323 Z= 0.162 Angle : 0.661 10.211 19399 Z= 0.338 Chirality : 0.042 0.249 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.320 51.578 1989 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.38 % Allowed : 33.69 % Favored : 59.93 % 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: 1.26 (0.19), residues: 1822 helix: 1.50 (0.13), residues: 1469 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG V 86 TYR 0.024 0.002 TYR I 48 PHE 0.019 0.001 PHE L 62 TRP 0.009 0.001 TRP T 208 HIS 0.003 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00354 (14321) covalent geometry : angle 0.66086 (19395) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.62211 ( 4) hydrogen bonds : bond 0.04847 ( 1238) hydrogen bonds : angle 3.85452 ( 3684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 303 time to evaluate : 0.569 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: symmetry clash revert: symmetry clash REVERT: Y 84 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.8932 (mm-40) REVERT: V 79 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8343 (mm) REVERT: V 130 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7429 (p0) REVERT: V 131 LEU cc_start: 0.8596 (mt) cc_final: 0.8204 (pp) REVERT: X 18 PHE cc_start: 0.9341 (t80) cc_final: 0.8887 (t80) REVERT: X 74 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8796 (tm-30) REVERT: X 78 LYS cc_start: 0.8011 (pttm) cc_final: 0.7744 (pttm) REVERT: X 115 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8720 (tm-30) REVERT: U 23 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6613 (t80) REVERT: I 11 LEU cc_start: 0.9089 (tp) cc_final: 0.8853 (tt) REVERT: J 61 ILE cc_start: 0.9173 (mm) cc_final: 0.8955 (pt) REVERT: K 1 MET cc_start: 0.8155 (tpt) cc_final: 0.7617 (tpp) REVERT: L 33 GLN cc_start: 0.9290 (mt0) cc_final: 0.8914 (mm110) REVERT: M 41 ILE cc_start: 0.8674 (tp) cc_final: 0.8306 (tt) REVERT: M 70 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8515 (mp) REVERT: O 1 MET cc_start: 0.6872 (tpt) cc_final: 0.6613 (tpt) REVERT: O 49 MET cc_start: 0.9186 (tmm) cc_final: 0.8870 (tmm) REVERT: P 42 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7943 (pp20) REVERT: T 85 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: T 122 TRP cc_start: 0.9273 (m-10) cc_final: 0.9001 (m-10) REVERT: Z 92 TYR cc_start: 0.9204 (t80) cc_final: 0.8937 (t80) REVERT: Z 195 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9110 (t80) REVERT: Z 223 ASN cc_start: 0.7778 (t0) cc_final: 0.7569 (m-40) REVERT: Z 277 TYR cc_start: 0.9250 (m-80) cc_final: 0.8670 (m-80) REVERT: Z 280 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8601 (tm-30) outliers start: 90 outliers final: 68 residues processed: 355 average time/residue: 0.1078 time to fit residues: 58.2313 Evaluate side-chains 370 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 127 GLN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 63 ARG Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 118 optimal weight: 0.5980 chunk 67 optimal weight: 0.0170 chunk 71 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 GLN U 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076308 restraints weight = 48024.813| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.69 r_work: 0.3309 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14323 Z= 0.143 Angle : 0.656 11.946 19399 Z= 0.335 Chirality : 0.043 0.343 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.310 52.171 1989 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.46 % Allowed : 34.68 % Favored : 59.86 % 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: 1.26 (0.19), residues: 1822 helix: 1.53 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -2.13 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG V 86 TYR 0.019 0.002 TYR P 48 PHE 0.020 0.001 PHE T 202 TRP 0.011 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00304 (14321) covalent geometry : angle 0.65588 (19395) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.61045 ( 4) hydrogen bonds : bond 0.04698 ( 1238) hydrogen bonds : angle 3.82941 ( 3684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 0.424 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: symmetry clash revert: symmetry clash REVERT: Y 84 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.8943 (mm-40) REVERT: V 79 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8366 (mm) REVERT: X 18 PHE cc_start: 0.9328 (t80) cc_final: 0.8860 (t80) REVERT: X 74 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8762 (tm-30) REVERT: X 78 LYS cc_start: 0.8028 (pttm) cc_final: 0.7762 (pttm) REVERT: X 115 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8586 (tm-30) REVERT: U 108 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8821 (mp0) REVERT: K 1 MET cc_start: 0.8163 (tpt) cc_final: 0.7579 (tpp) REVERT: K 33 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8641 (mm-40) REVERT: L 33 GLN cc_start: 0.9308 (mt0) cc_final: 0.8933 (mm110) REVERT: M 41 ILE cc_start: 0.8613 (tp) cc_final: 0.8234 (tt) REVERT: M 70 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8478 (mp) REVERT: O 1 MET cc_start: 0.6678 (tpt) cc_final: 0.6420 (tpt) REVERT: O 49 MET cc_start: 0.9178 (tmm) cc_final: 0.8857 (tmm) REVERT: P 42 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7899 (pp20) REVERT: T 22 ARG cc_start: 0.6551 (ptt-90) cc_final: 0.5986 (ptp90) REVERT: T 85 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: T 122 TRP cc_start: 0.9273 (m-10) cc_final: 0.8998 (m-10) REVERT: Z 195 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9038 (t80) REVERT: Z 277 TYR cc_start: 0.9225 (m-80) cc_final: 0.8656 (m-80) REVERT: Z 280 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8619 (tm-30) outliers start: 77 outliers final: 67 residues processed: 361 average time/residue: 0.1033 time to fit residues: 57.4168 Evaluate side-chains 372 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 17 ASN Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 161 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 90 GLN ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075778 restraints weight = 47932.739| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.66 r_work: 0.3294 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14323 Z= 0.154 Angle : 0.699 12.128 19399 Z= 0.355 Chirality : 0.044 0.313 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.329 52.124 1989 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.25 % Allowed : 35.96 % Favored : 58.79 % 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: 1.25 (0.19), residues: 1822 helix: 1.51 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 117 TYR 0.025 0.002 TYR I 48 PHE 0.021 0.001 PHE Y 11 TRP 0.010 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00338 (14321) covalent geometry : angle 0.69950 (19395) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.56837 ( 4) hydrogen bonds : bond 0.04737 ( 1238) hydrogen bonds : angle 3.84653 ( 3684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3644 Ramachandran restraints generated. 1822 Oldfield, 0 Emsley, 1822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 0.538 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 84 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.8946 (mm-40) REVERT: V 79 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8334 (mm) REVERT: X 18 PHE cc_start: 0.9323 (t80) cc_final: 0.8878 (t80) REVERT: X 74 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8766 (tm-30) REVERT: X 78 LYS cc_start: 0.8019 (pttm) cc_final: 0.7747 (pttm) REVERT: X 115 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8580 (tm-30) REVERT: U 108 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8790 (mp0) REVERT: I 1 MET cc_start: 0.6462 (mmm) cc_final: 0.6023 (mtp) REVERT: K 1 MET cc_start: 0.8138 (tpt) cc_final: 0.7599 (tpp) REVERT: K 2 GLU cc_start: 0.8623 (pm20) cc_final: 0.8377 (pm20) REVERT: K 33 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8655 (mm-40) REVERT: L 33 GLN cc_start: 0.9300 (mt0) cc_final: 0.8921 (mm110) REVERT: M 41 ILE cc_start: 0.8624 (tp) cc_final: 0.8246 (tt) REVERT: M 70 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8527 (mp) REVERT: O 1 MET cc_start: 0.6687 (tpt) cc_final: 0.6446 (tpt) REVERT: O 49 MET cc_start: 0.9200 (tmm) cc_final: 0.8884 (tmm) REVERT: P 42 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7927 (pp20) REVERT: T 22 ARG cc_start: 0.6551 (ptt-90) cc_final: 0.5982 (ptp90) REVERT: T 85 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: T 122 TRP cc_start: 0.9257 (m-10) cc_final: 0.9002 (m-10) REVERT: Z 33 GLU cc_start: 0.8164 (mp0) cc_final: 0.7938 (mp0) REVERT: Z 195 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.9009 (t80) REVERT: Z 277 TYR cc_start: 0.9254 (m-80) cc_final: 0.8682 (m-80) REVERT: Z 280 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8635 (tm-30) outliers start: 74 outliers final: 65 residues processed: 349 average time/residue: 0.1048 time to fit residues: 55.6625 Evaluate side-chains 376 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 305 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 63 ARG Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 268 VAL Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 174 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.0050 chunk 103 optimal weight: 0.7980 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 90 GLN ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.098385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077360 restraints weight = 48100.102| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.75 r_work: 0.3329 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14323 Z= 0.143 Angle : 0.700 19.873 19399 Z= 0.349 Chirality : 0.043 0.300 2334 Planarity : 0.005 0.081 2483 Dihedral : 4.309 52.771 1989 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.89 % Allowed : 36.24 % Favored : 58.87 % 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: 1.27 (0.19), residues: 1822 helix: 1.52 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 119 TYR 0.024 0.002 TYR I 48 PHE 0.019 0.001 PHE T 202 TRP 0.011 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00304 (14321) covalent geometry : angle 0.69995 (19395) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.56745 ( 4) hydrogen bonds : bond 0.04595 ( 1238) hydrogen bonds : angle 3.81730 ( 3684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3991.37 seconds wall clock time: 68 minutes 55.04 seconds (4135.04 seconds total)