Starting phenix.real_space_refine on Thu Jun 12 14:20:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itn_60872/06_2025/9itn_60872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itn_60872/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9itn_60872/06_2025/9itn_60872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itn_60872/06_2025/9itn_60872.map" model { file = "/net/cci-nas-00/data/ceres_data/9itn_60872/06_2025/9itn_60872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itn_60872/06_2025/9itn_60872.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.61, per 1000 atoms: 0.68 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: 3.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.02 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: 4.72 Time building geometry restraints manager: 4.40 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: 0.010 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.540 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP T 122 HIS 0.011 0.001 HIS V 149 PHE 0.041 0.002 PHE Z 123 TYR 0.031 0.002 TYR U 65 ARG 0.014 0.000 ARG Y 119 Details of bonding type rmsd hydrogen bonds : bond 0.13403 ( 1238) hydrogen bonds : angle 5.93637 ( 3684) SS BOND : bond 0.87643 ( 2) SS BOND : angle 25.57229 ( 4) covalent geometry : bond 0.00474 (14321) covalent geometry : angle 0.83329 (19395) *********************** 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 : 1.569 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: 0.2571 time to fit residues: 127.7377 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 : 1.562 ------------------------------------------------------------------------------- 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 153 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 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** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 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 = 0.3915 r_free = 0.3915 target = 0.097766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076494 restraints weight = 47907.220| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.72 r_work: 0.3306 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14323 Z= 0.156 Angle : 0.601 8.766 19399 Z= 0.322 Chirality : 0.041 0.184 2334 Planarity : 0.005 0.085 2483 Dihedral : 4.852 50.296 1998 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.11 % Allowed : 30.71 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1822 helix: 1.09 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 208 HIS 0.008 0.001 HIS V 149 PHE 0.029 0.001 PHE Z 123 TYR 0.027 0.002 TYR N 48 ARG 0.007 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.05283 ( 1238) hydrogen bonds : angle 4.20754 ( 3684) SS BOND : bond 0.01940 ( 2) SS BOND : angle 2.85218 ( 4) covalent geometry : bond 0.00319 (14321) covalent geometry : angle 0.59940 (19395) *********************** 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 423 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 351 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 119 ARG cc_start: 0.8819 (tmm160) cc_final: 0.8582 (ttp80) REVERT: V 79 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8343 (mm) REVERT: V 130 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7621 (p0) REVERT: X 18 PHE cc_start: 0.9298 (t80) cc_final: 0.8897 (t80) REVERT: X 85 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9099 (mm-30) REVERT: U 34 MET cc_start: 0.8563 (pmm) cc_final: 0.8314 (pmm) REVERT: U 117 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6463 (ttp80) REVERT: I 57 GLU cc_start: 0.9384 (tp30) cc_final: 0.9152 (tp30) REVERT: M 57 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8701 (mm-30) REVERT: O 49 MET cc_start: 0.9201 (tmm) cc_final: 0.8981 (tmm) REVERT: T 85 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: T 122 TRP cc_start: 0.9250 (m-10) cc_final: 0.8948 (m-10) REVERT: Z 33 GLU cc_start: 0.7869 (mp0) cc_final: 0.7512 (mp0) REVERT: Z 74 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8459 (tm-30) REVERT: Z 85 GLU cc_start: 0.9144 (tt0) cc_final: 0.8895 (tt0) REVERT: Z 92 TYR cc_start: 0.9296 (t80) cc_final: 0.8930 (t80) REVERT: Z 206 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8994 (mm-30) outliers start: 72 outliers final: 41 residues processed: 391 average time/residue: 0.2349 time to fit residues: 137.2733 Evaluate side-chains 353 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 I residue 65 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 13 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 235 GLU 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 58 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 130 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 0.0170 chunk 173 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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 U 84 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 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 = 0.3904 r_free = 0.3904 target = 0.097208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075951 restraints weight = 48077.571| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.71 r_work: 0.3304 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14323 Z= 0.152 Angle : 0.594 9.523 19399 Z= 0.315 Chirality : 0.041 0.195 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.483 52.501 1992 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.17 % Allowed : 31.13 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1822 helix: 1.25 (0.13), residues: 1461 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP T 208 HIS 0.006 0.001 HIS V 149 PHE 0.022 0.001 PHE Z 123 TYR 0.026 0.002 TYR N 48 ARG 0.006 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 1238) hydrogen bonds : angle 4.00952 ( 3684) SS BOND : bond 0.00730 ( 2) SS BOND : angle 1.43620 ( 4) covalent geometry : bond 0.00319 (14321) covalent geometry : angle 0.59335 (19395) *********************** 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 415 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 328 time to evaluate : 1.636 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 90 GLN cc_start: 0.8865 (mt0) cc_final: 0.8662 (mt0) REVERT: V 79 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8365 (mm) REVERT: V 130 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7566 (p0) REVERT: V 131 LEU cc_start: 0.8659 (mt) cc_final: 0.8244 (pp) REVERT: X 18 PHE cc_start: 0.9294 (t80) cc_final: 0.8926 (t80) REVERT: X 85 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9124 (mm-30) REVERT: X 115 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8660 (tm-30) REVERT: U 34 MET cc_start: 0.8673 (pmm) cc_final: 0.8391 (pmm) REVERT: I 57 GLU cc_start: 0.9409 (tp30) cc_final: 0.9146 (tp30) REVERT: L 33 GLN cc_start: 0.9278 (mt0) cc_final: 0.8985 (mm-40) REVERT: M 41 ILE cc_start: 0.8584 (tp) cc_final: 0.8329 (tt) REVERT: O 49 MET cc_start: 0.9172 (tmm) cc_final: 0.8904 (tmm) REVERT: Q 37 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8416 (mpt-90) REVERT: T 122 TRP cc_start: 0.9302 (m-10) cc_final: 0.8987 (m-10) REVERT: T 294 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9349 (mm) REVERT: Z 85 GLU cc_start: 0.9171 (tt0) cc_final: 0.8868 (tt0) REVERT: Z 92 TYR cc_start: 0.9291 (t80) cc_final: 0.8904 (t80) REVERT: Z 206 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9021 (mm-30) REVERT: Z 267 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8164 (mm) REVERT: Z 280 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8573 (tm-30) outliers start: 87 outliers final: 56 residues processed: 378 average time/residue: 0.2319 time to fit residues: 130.7792 Evaluate side-chains 365 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 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 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 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 55 PHE 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 O residue 65 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 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 18 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 168 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 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 = 0.3918 r_free = 0.3918 target = 0.097963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076838 restraints weight = 47721.645| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.72 r_work: 0.3311 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14323 Z= 0.140 Angle : 0.588 8.440 19399 Z= 0.309 Chirality : 0.040 0.201 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.274 50.845 1989 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.45 % Allowed : 30.43 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1822 helix: 1.31 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 208 HIS 0.006 0.001 HIS V 149 PHE 0.019 0.001 PHE Z 123 TYR 0.022 0.002 TYR N 48 ARG 0.005 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 1238) hydrogen bonds : angle 3.90803 ( 3684) SS BOND : bond 0.00025 ( 2) SS BOND : angle 0.88956 ( 4) covalent geometry : bond 0.00292 (14321) covalent geometry : angle 0.58777 (19395) *********************** 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 425 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 334 time to evaluate : 1.474 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 119 ARG cc_start: 0.8801 (tmm160) cc_final: 0.8564 (ttp80) REVERT: V 79 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8373 (mm) REVERT: V 130 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7489 (p0) REVERT: V 131 LEU cc_start: 0.8649 (mt) cc_final: 0.8263 (pp) REVERT: X 18 PHE cc_start: 0.9303 (t80) cc_final: 0.8870 (t80) REVERT: X 115 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8607 (tm-30) REVERT: U 34 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8407 (pmm) REVERT: U 117 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6710 (ttp80) REVERT: I 57 GLU cc_start: 0.9396 (tp30) cc_final: 0.9179 (tp30) REVERT: L 33 GLN cc_start: 0.9266 (mt0) cc_final: 0.8922 (mm110) REVERT: M 37 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7693 (ttm-80) REVERT: M 41 ILE cc_start: 0.8587 (tp) cc_final: 0.8268 (tt) REVERT: O 1 MET cc_start: 0.6591 (tpt) cc_final: 0.6131 (tpt) REVERT: O 49 MET cc_start: 0.9187 (tmm) cc_final: 0.8770 (tmm) REVERT: P 42 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: T 85 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: T 122 TRP cc_start: 0.9303 (m-10) cc_final: 0.8846 (m100) REVERT: Z 85 GLU cc_start: 0.9119 (tt0) cc_final: 0.8806 (tt0) REVERT: Z 267 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8233 (mm) REVERT: Z 280 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8541 (tm-30) outliers start: 91 outliers final: 64 residues processed: 386 average time/residue: 0.2362 time to fit residues: 135.5006 Evaluate side-chains 381 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 U residue 23 PHE Chi-restraints excluded: chain U residue 30 TYR Chi-restraints excluded: chain U residue 34 MET 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 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 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 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 26 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 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 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 264 MET Chi-restraints excluded: chain T residue 274 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 65 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.096513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075212 restraints weight = 48242.564| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.74 r_work: 0.3275 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14323 Z= 0.169 Angle : 0.628 12.231 19399 Z= 0.325 Chirality : 0.042 0.249 2334 Planarity : 0.005 0.081 2483 Dihedral : 4.255 50.974 1989 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.74 % Allowed : 32.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 1822 helix: 1.38 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.006 0.001 HIS V 149 PHE 0.018 0.001 PHE L 62 TYR 0.021 0.002 TYR N 48 ARG 0.010 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 1238) hydrogen bonds : angle 3.90126 ( 3684) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.78763 ( 4) covalent geometry : bond 0.00370 (14321) covalent geometry : angle 0.62799 (19395) *********************** 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 408 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 313 time to evaluate : 1.454 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 119 ARG cc_start: 0.8816 (tmm160) cc_final: 0.8410 (tmm160) REVERT: V 79 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8353 (mm) REVERT: V 130 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7525 (p0) REVERT: V 131 LEU cc_start: 0.8656 (mt) cc_final: 0.8251 (pp) REVERT: X 18 PHE cc_start: 0.9324 (t80) cc_final: 0.8935 (t80) REVERT: X 74 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8763 (tm-30) REVERT: X 78 LYS cc_start: 0.8059 (pttm) cc_final: 0.7779 (pttm) REVERT: X 115 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8623 (tm-30) REVERT: X 120 MET cc_start: 0.8841 (tpt) cc_final: 0.8497 (tpt) REVERT: U 34 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8414 (pmm) REVERT: U 117 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6789 (ttp80) REVERT: L 33 GLN cc_start: 0.9292 (mt0) cc_final: 0.8932 (mm110) REVERT: L 61 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8501 (mm) REVERT: M 37 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7609 (ttm-80) REVERT: M 41 ILE cc_start: 0.8631 (tp) cc_final: 0.8231 (tt) REVERT: M 48 TYR cc_start: 0.8502 (m-10) cc_final: 0.8114 (m-10) REVERT: O 1 MET cc_start: 0.6661 (tpt) cc_final: 0.6333 (tpt) REVERT: O 49 MET cc_start: 0.9205 (tmm) cc_final: 0.8758 (tmm) REVERT: P 42 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: T 85 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: T 122 TRP cc_start: 0.9278 (m-10) cc_final: 0.9012 (m-10) REVERT: Z 92 TYR cc_start: 0.9319 (t80) cc_final: 0.9080 (t80) REVERT: Z 267 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8327 (mm) REVERT: Z 280 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8547 (tm-30) outliers start: 95 outliers final: 68 residues processed: 363 average time/residue: 0.2303 time to fit residues: 124.5330 Evaluate side-chains 381 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 303 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 LEU 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 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 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 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 45 VAL 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 11 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 61 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 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 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 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 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 267 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 0.0370 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 ** 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 = 0.3910 r_free = 0.3910 target = 0.097569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076398 restraints weight = 48526.103| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.77 r_work: 0.3301 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14323 Z= 0.143 Angle : 0.611 9.900 19399 Z= 0.316 Chirality : 0.042 0.423 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.264 51.597 1989 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.67 % Allowed : 33.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 1822 helix: 1.41 (0.13), residues: 1469 sheet: None (None), residues: 0 loop : -1.98 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 208 HIS 0.006 0.001 HIS V 149 PHE 0.016 0.001 PHE L 62 TYR 0.019 0.002 TYR H 48 ARG 0.012 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1238) hydrogen bonds : angle 3.83740 ( 3684) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.68827 ( 4) covalent geometry : bond 0.00304 (14321) covalent geometry : angle 0.61058 (19395) *********************** 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 412 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 318 time to evaluate : 1.386 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: V 79 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8365 (mm) REVERT: V 130 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7536 (p0) REVERT: X 18 PHE cc_start: 0.9319 (t80) cc_final: 0.8903 (t80) REVERT: X 74 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8736 (tm-30) REVERT: X 78 LYS cc_start: 0.8044 (pttm) cc_final: 0.7754 (pttm) REVERT: X 115 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8605 (tm-30) REVERT: X 120 MET cc_start: 0.8832 (tpt) cc_final: 0.8498 (tpt) REVERT: U 117 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6776 (ttp80) REVERT: L 33 GLN cc_start: 0.9311 (mt0) cc_final: 0.8964 (mm110) REVERT: M 37 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7667 (ttm-80) REVERT: M 41 ILE cc_start: 0.8684 (tp) cc_final: 0.8265 (tt) REVERT: O 1 MET cc_start: 0.6659 (tpt) cc_final: 0.6316 (tpt) REVERT: O 49 MET cc_start: 0.9217 (tmm) cc_final: 0.8962 (tmm) REVERT: P 42 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: T 85 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: T 122 TRP cc_start: 0.9283 (m-10) cc_final: 0.9012 (m-10) REVERT: T 185 ARG cc_start: 0.7310 (tpt-90) cc_final: 0.6926 (tpt-90) REVERT: Z 92 TYR cc_start: 0.9312 (t80) cc_final: 0.9098 (t80) REVERT: Z 267 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8442 (mm) REVERT: Z 280 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8560 (tm-30) outliers start: 94 outliers final: 65 residues processed: 371 average time/residue: 0.2326 time to fit residues: 127.0622 Evaluate side-chains 375 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 302 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 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 139 VAL 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 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 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 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 53 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 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 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 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 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 264 MET Chi-restraints excluded: chain T residue 274 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 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 43 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** X 127 GLN U 74 GLN U 84 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.094923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.073609 restraints weight = 48572.214| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.66 r_work: 0.3237 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14323 Z= 0.198 Angle : 0.658 12.104 19399 Z= 0.344 Chirality : 0.042 0.267 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.329 50.958 1989 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 7.09 % Allowed : 33.12 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1822 helix: 1.44 (0.13), residues: 1454 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Z 208 HIS 0.003 0.001 HIS V 149 PHE 0.020 0.001 PHE L 62 TYR 0.020 0.002 TYR I 48 ARG 0.014 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 1238) hydrogen bonds : angle 3.93306 ( 3684) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.68549 ( 4) covalent geometry : bond 0.00441 (14321) covalent geometry : angle 0.65825 (19395) *********************** 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 405 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 305 time to evaluate : 1.701 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: 0.9389 (OUTLIER) cc_final: 0.9059 (mm-40) REVERT: Y 119 ARG cc_start: 0.8822 (tmm160) cc_final: 0.8610 (ttp80) REVERT: V 46 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8625 (tm-30) REVERT: V 79 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8405 (mm) REVERT: V 131 LEU cc_start: 0.8667 (mt) cc_final: 0.8296 (pp) REVERT: X 18 PHE cc_start: 0.9353 (t80) cc_final: 0.8964 (t80) REVERT: X 74 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: X 78 LYS cc_start: 0.8010 (pttm) cc_final: 0.7735 (pttm) REVERT: X 106 LYS cc_start: 0.9347 (ptpp) cc_final: 0.9120 (ptpp) REVERT: U 103 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8795 (tm-30) REVERT: J 61 ILE cc_start: 0.9173 (mm) cc_final: 0.8931 (pt) REVERT: K 1 MET cc_start: 0.8073 (tpt) cc_final: 0.7592 (tpp) REVERT: L 33 GLN cc_start: 0.9291 (mt0) cc_final: 0.8744 (tm-30) REVERT: M 41 ILE cc_start: 0.8686 (tp) cc_final: 0.8355 (tt) REVERT: O 1 MET cc_start: 0.6988 (tpt) cc_final: 0.6714 (tpt) REVERT: O 49 MET cc_start: 0.9171 (tmm) cc_final: 0.8849 (tmm) REVERT: P 42 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7966 (pp20) REVERT: T 85 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: T 122 TRP cc_start: 0.9265 (m-10) cc_final: 0.9007 (m-10) REVERT: Z 92 TYR cc_start: 0.9304 (t80) cc_final: 0.9094 (t80) REVERT: Z 280 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8519 (tm-30) outliers start: 100 outliers final: 73 residues processed: 361 average time/residue: 0.3017 time to fit residues: 163.7846 Evaluate side-chains 374 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 294 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 84 GLN 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 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 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 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 H residue 56 THR 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 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 18 ILE Chi-restraints excluded: chain K residue 45 VAL 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 53 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 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 56 THR Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU 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 264 MET 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 205 ILE 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 117 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 158 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.097309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075629 restraints weight = 48006.891| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.73 r_work: 0.3293 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14323 Z= 0.145 Angle : 0.654 10.888 19399 Z= 0.335 Chirality : 0.042 0.256 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.329 52.159 1989 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.89 % Allowed : 34.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1822 helix: 1.47 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.018 0.001 PHE L 62 TYR 0.021 0.002 TYR P 48 ARG 0.014 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 1238) hydrogen bonds : angle 3.85738 ( 3684) SS BOND : bond 0.00016 ( 2) SS BOND : angle 0.66941 ( 4) covalent geometry : bond 0.00306 (14321) covalent geometry : angle 0.65351 (19395) *********************** 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 400 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 1.610 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: 0.9387 (OUTLIER) cc_final: 0.8909 (mm-40) REVERT: Y 119 ARG cc_start: 0.8832 (tmm160) cc_final: 0.8607 (ttp80) REVERT: V 79 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8349 (mm) REVERT: X 18 PHE cc_start: 0.9364 (t80) cc_final: 0.8865 (t80) REVERT: X 74 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8762 (tm-30) REVERT: X 78 LYS cc_start: 0.7961 (pttm) cc_final: 0.7700 (pttm) REVERT: X 106 LYS cc_start: 0.9323 (ptpp) cc_final: 0.9102 (ptpp) REVERT: X 120 MET cc_start: 0.8820 (tpt) cc_final: 0.8488 (tpt) REVERT: U 117 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6924 (ttp80) REVERT: J 61 ILE cc_start: 0.9167 (mm) cc_final: 0.8935 (pt) REVERT: K 1 MET cc_start: 0.8094 (tpt) cc_final: 0.7599 (tpp) REVERT: L 33 GLN cc_start: 0.9301 (mt0) cc_final: 0.8789 (tm-30) REVERT: M 41 ILE cc_start: 0.8640 (tp) cc_final: 0.8281 (tt) REVERT: O 1 MET cc_start: 0.6759 (tpt) cc_final: 0.6519 (tpt) REVERT: O 49 MET cc_start: 0.9192 (tmm) cc_final: 0.8874 (tmm) REVERT: P 42 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7915 (pp20) REVERT: T 85 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: T 122 TRP cc_start: 0.9264 (m-10) cc_final: 0.8996 (m-10) REVERT: Z 33 GLU cc_start: 0.8186 (mp0) cc_final: 0.7974 (mp0) REVERT: Z 125 LEU cc_start: 0.9147 (mt) cc_final: 0.8823 (mp) REVERT: Z 195 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9121 (t80) REVERT: Z 277 TYR cc_start: 0.9193 (m-80) cc_final: 0.8526 (m-80) REVERT: Z 280 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8503 (tm-30) outliers start: 83 outliers final: 63 residues processed: 366 average time/residue: 0.2327 time to fit residues: 127.1405 Evaluate side-chains 370 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 300 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 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 I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET 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 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 53 ILE Chi-restraints excluded: chain L residue 57 GLU 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** X 127 GLN U 74 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 = 0.3898 r_free = 0.3898 target = 0.097020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075878 restraints weight = 47965.248| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.67 r_work: 0.3290 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2281 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= 0.151 Angle : 0.660 10.555 19399 Z= 0.338 Chirality : 0.042 0.257 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.295 51.890 1989 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.60 % Allowed : 34.33 % Favored : 60.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1822 helix: 1.49 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.021 0.001 PHE Z 251 TYR 0.022 0.002 TYR I 48 ARG 0.016 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 1238) hydrogen bonds : angle 3.84251 ( 3684) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.60548 ( 4) covalent geometry : bond 0.00329 (14321) covalent geometry : angle 0.66031 (19395) *********************** 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 390 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 311 time to evaluate : 1.498 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: 0.9395 (OUTLIER) cc_final: 0.8921 (mm-40) REVERT: Y 119 ARG cc_start: 0.8833 (tmm160) cc_final: 0.8602 (ttp80) REVERT: V 46 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8631 (tm-30) REVERT: V 79 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8343 (mm) REVERT: X 18 PHE cc_start: 0.9360 (t80) cc_final: 0.8866 (t80) REVERT: X 120 MET cc_start: 0.8873 (tpt) cc_final: 0.8540 (tpt) REVERT: U 108 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8781 (mp0) REVERT: U 117 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6736 (ttp80) REVERT: J 61 ILE cc_start: 0.9165 (mm) cc_final: 0.8931 (pt) REVERT: K 1 MET cc_start: 0.8087 (tpt) cc_final: 0.7591 (tpp) REVERT: L 33 GLN cc_start: 0.9289 (mt0) cc_final: 0.8772 (tm-30) REVERT: M 41 ILE cc_start: 0.8635 (tp) cc_final: 0.8278 (tt) REVERT: O 1 MET cc_start: 0.6726 (tpt) cc_final: 0.6417 (tpt) REVERT: O 49 MET cc_start: 0.9213 (tmm) cc_final: 0.8894 (tmm) REVERT: P 42 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: T 85 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: T 122 TRP cc_start: 0.9272 (m-10) cc_final: 0.9004 (m-10) REVERT: T 242 LYS cc_start: 0.9407 (mmtp) cc_final: 0.8967 (mmtp) REVERT: Z 33 GLU cc_start: 0.8162 (mp0) cc_final: 0.7955 (mp0) REVERT: Z 92 TYR cc_start: 0.9247 (t80) cc_final: 0.8899 (t80) REVERT: Z 125 LEU cc_start: 0.9106 (mt) cc_final: 0.8834 (mp) REVERT: Z 223 ASN cc_start: 0.7716 (t0) cc_final: 0.7515 (m-40) REVERT: Z 277 TYR cc_start: 0.9177 (m-80) cc_final: 0.8562 (m-80) REVERT: Z 280 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 79 outliers final: 64 residues processed: 358 average time/residue: 0.2324 time to fit residues: 124.7181 Evaluate side-chains 377 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 84 GLN 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 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 131 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU 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 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 I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET 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 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 53 ILE Chi-restraints excluded: chain L residue 57 GLU 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 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 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 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 12 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 175 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.096693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075547 restraints weight = 48284.598| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.67 r_work: 0.3289 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14323 Z= 0.153 Angle : 0.686 11.549 19399 Z= 0.351 Chirality : 0.043 0.249 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.327 52.073 1989 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.32 % Allowed : 35.18 % Favored : 59.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1822 helix: 1.47 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.020 0.001 PHE L 62 TYR 0.019 0.002 TYR P 48 ARG 0.017 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 1238) hydrogen bonds : angle 3.86895 ( 3684) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.58637 ( 4) covalent geometry : bond 0.00336 (14321) covalent geometry : angle 0.68587 (19395) ********************** 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 388 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 313 time to evaluate : 1.490 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: 0.9407 (OUTLIER) cc_final: 0.8932 (mm-40) REVERT: Y 119 ARG cc_start: 0.8834 (tmm160) cc_final: 0.8601 (ttp80) REVERT: V 46 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: V 79 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8374 (mm) REVERT: X 18 PHE cc_start: 0.9345 (t80) cc_final: 0.8859 (t80) REVERT: X 115 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8747 (tm-30) REVERT: X 120 MET cc_start: 0.8863 (tpt) cc_final: 0.8535 (tpt) REVERT: U 108 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8774 (mp0) REVERT: U 117 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6711 (ttp80) REVERT: I 1 MET cc_start: 0.6544 (mmm) cc_final: 0.6121 (mtp) REVERT: J 61 ILE cc_start: 0.9157 (mm) cc_final: 0.8946 (pt) REVERT: K 1 MET cc_start: 0.8041 (tpt) cc_final: 0.7560 (tpp) REVERT: K 2 GLU cc_start: 0.8650 (pm20) cc_final: 0.8391 (pm20) REVERT: L 33 GLN cc_start: 0.9284 (mt0) cc_final: 0.8769 (tm-30) REVERT: M 41 ILE cc_start: 0.8638 (tp) cc_final: 0.8279 (tt) REVERT: O 1 MET cc_start: 0.6729 (tpt) cc_final: 0.6423 (tpt) REVERT: O 49 MET cc_start: 0.9232 (tmm) cc_final: 0.8920 (tmm) REVERT: P 42 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: T 85 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: T 122 TRP cc_start: 0.9276 (m-10) cc_final: 0.9007 (m-10) REVERT: T 242 LYS cc_start: 0.9409 (mmtp) cc_final: 0.8966 (mmtp) REVERT: Z 92 TYR cc_start: 0.9222 (t80) cc_final: 0.8871 (t80) REVERT: Z 125 LEU cc_start: 0.9104 (mt) cc_final: 0.8840 (mp) REVERT: Z 195 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9058 (t80) REVERT: Z 223 ASN cc_start: 0.7748 (t0) cc_final: 0.7539 (m-40) REVERT: Z 255 PHE cc_start: 0.9118 (t80) cc_final: 0.8880 (t80) REVERT: Z 277 TYR cc_start: 0.9167 (m-80) cc_final: 0.8551 (m-80) REVERT: Z 280 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8447 (tm-30) outliers start: 75 outliers final: 65 residues processed: 355 average time/residue: 0.2481 time to fit residues: 131.2218 Evaluate side-chains 382 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 310 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 84 GLN 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 130 ASP Chi-restraints excluded: chain X residue 12 ILE 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 131 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU 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 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 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 56 THR 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 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 53 ILE Chi-restraints excluded: chain L residue 57 GLU 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 10 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 140 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.097305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076179 restraints weight = 48626.409| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.70 r_work: 0.3298 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14323 Z= 0.147 Angle : 0.684 11.405 19399 Z= 0.349 Chirality : 0.042 0.240 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.320 52.377 1989 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.25 % Allowed : 35.46 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1822 helix: 1.49 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.029 0.001 PHE T 255 TYR 0.024 0.002 TYR I 48 ARG 0.017 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 1238) hydrogen bonds : angle 3.84771 ( 3684) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.55063 ( 4) covalent geometry : bond 0.00319 (14321) covalent geometry : angle 0.68440 (19395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8334.52 seconds wall clock time: 145 minutes 53.30 seconds (8753.30 seconds total)