Starting phenix.real_space_refine on Fri May 16 04:11:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itn_60872/05_2025/9itn_60872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itn_60872/05_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_60872/05_2025/9itn_60872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itn_60872/05_2025/9itn_60872.map" model { file = "/net/cci-nas-00/data/ceres_data/9itn_60872/05_2025/9itn_60872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itn_60872/05_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-5687/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: 8.62, per 1000 atoms: 0.61 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 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: 0.99 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: 3.90 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4644 1.34 - 1.46: 2848 1.46 - 1.58: 6755 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 14321 Sorted by residual: bond pdb=" N ILE O 70 " pdb=" CA ILE O 70 " ideal model delta sigma weight residual 1.460 1.496 -0.035 1.19e-02 7.06e+03 8.88e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.56e+00 bond pdb=" N ILE P 66 " pdb=" CA ILE P 66 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.82e+00 bond pdb=" N ILE P 70 " pdb=" CA ILE P 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.71e+00 bond pdb=" N VAL P 65 " pdb=" CA VAL P 65 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.54e+00 ... (remaining 14316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 18748 2.08 - 4.15: 519 4.15 - 6.23: 93 6.23 - 8.31: 25 8.31 - 10.38: 10 Bond angle restraints: 19395 Sorted by residual: angle pdb=" N LEU X 121 " pdb=" CA LEU X 121 " pdb=" C LEU X 121 " ideal model delta sigma weight residual 111.14 105.97 5.17 1.08e+00 8.57e-01 2.29e+01 angle pdb=" CA LYS X 78 " pdb=" CB LYS X 78 " pdb=" CG LYS X 78 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.97e+01 angle pdb=" N ARG V 86 " pdb=" CA ARG V 86 " pdb=" C ARG V 86 " ideal model delta sigma weight residual 113.01 107.99 5.02 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA GLN Z 74 " pdb=" CB GLN Z 74 " pdb=" CG GLN Z 74 " ideal model delta sigma weight residual 114.10 122.36 -8.26 2.00e+00 2.50e-01 1.70e+01 angle pdb=" N ILE M 70 " pdb=" CA ILE M 70 " pdb=" C ILE M 70 " ideal model delta sigma weight residual 113.42 108.65 4.77 1.17e+00 7.31e-01 1.67e+01 ... (remaining 19390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7172 17.93 - 35.87: 997 35.87 - 53.80: 266 53.80 - 71.73: 40 71.73 - 89.67: 25 Dihedral angle restraints: 8500 sinusoidal: 3253 harmonic: 5247 Sorted by residual: dihedral pdb=" CA MET U 34 " pdb=" C MET U 34 " pdb=" N ASN U 35 " pdb=" CA ASN U 35 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CB CYS T 135 " pdb=" SG CYS T 135 " pdb=" SG CYS T 173 " pdb=" CB CYS T 173 " ideal model delta sinusoidal sigma weight residual 93.00 50.84 42.16 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CA PHE T 52 " pdb=" C PHE T 52 " pdb=" N VAL T 53 " pdb=" CA VAL T 53 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 8497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1748 0.051 - 0.103: 475 0.103 - 0.154: 91 0.154 - 0.205: 15 0.205 - 0.257: 5 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CB VAL U 80 " pdb=" CA VAL U 80 " pdb=" CG1 VAL U 80 " pdb=" CG2 VAL U 80 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE T 200 " pdb=" CA ILE T 200 " pdb=" CG1 ILE T 200 " pdb=" CG2 ILE T 200 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE H 18 " pdb=" CA ILE H 18 " pdb=" CG1 ILE H 18 " pdb=" CG2 ILE H 18 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2331 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO Q 20 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 19 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO H 20 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO H 20 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 20 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY M 19 " -0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO M 20 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 20 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 20 " -0.038 5.00e-02 4.00e+02 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1908 2.75 - 3.29: 15826 3.29 - 3.83: 24977 3.83 - 4.36: 27238 4.36 - 4.90: 45940 Nonbonded interactions: 115889 Sorted by model distance: nonbonded pdb=" O ALA X 72 " pdb=" NH1 ARG U 71 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASN N 43 " pdb=" N ARG N 44 " model vdw 2.242 3.120 nonbonded pdb=" O ALA U 129 " pdb=" OG1 THR U 133 " model vdw 2.244 3.040 nonbonded pdb=" ND2 ASN V 17 " pdb=" OD2 ASP Z 59 " model vdw 2.270 3.120 nonbonded pdb=" O PHE T 86 " pdb=" OG SER T 90 " model vdw 2.292 3.040 ... (remaining 115884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = (chain 'I' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'K' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'M' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'N' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'O' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'P' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'Q' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) } ncs_group { reference = (chain 'T' and (resid 19 through 136 or resid 169 through 304)) selection = (chain 'Z' and resid 19 through 304) } ncs_group { reference = (chain 'U' and (resid 8 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 157)) selection = (chain 'V' and (resid 8 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 157)) selection = chain 'X' selection = (chain 'Y' and (resid 8 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 157)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.530 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- 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 : 1.453 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: 0.2407 time to fit residues: 118.9206 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 : 1.630 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076498 restraints weight = 47907.224| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.72 r_work: 0.3305 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 2.85217 ( 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 : 1.440 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: 0.8585 (ttp80) REVERT: V 79 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8343 (mm) REVERT: V 130 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7630 (p0) REVERT: X 18 PHE cc_start: 0.9299 (t80) cc_final: 0.8897 (t80) REVERT: X 85 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9106 (mm-30) REVERT: U 34 MET cc_start: 0.8563 (pmm) cc_final: 0.8315 (pmm) REVERT: U 117 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6462 (ttp80) REVERT: I 57 GLU cc_start: 0.9386 (tp30) cc_final: 0.9154 (tp30) REVERT: M 57 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8705 (mm-30) REVERT: O 49 MET cc_start: 0.9200 (tmm) cc_final: 0.8980 (tmm) REVERT: T 85 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: T 122 TRP cc_start: 0.9248 (m-10) cc_final: 0.8944 (m-10) REVERT: Z 33 GLU cc_start: 0.7874 (mp0) cc_final: 0.7517 (mp0) REVERT: Z 74 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: Z 85 GLU cc_start: 0.9147 (tt0) cc_final: 0.8900 (tt0) REVERT: Z 92 TYR cc_start: 0.9295 (t80) cc_final: 0.8927 (t80) REVERT: Z 206 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8988 (mm-30) outliers start: 72 outliers final: 41 residues processed: 391 average time/residue: 0.2262 time to fit residues: 131.5644 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 : 1.455 ------------------------------------------------------------------------------- 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: 2.9990 chunk 171 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.097030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075746 restraints weight = 48136.738| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.70 r_work: 0.3293 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1379 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= 0.157 Angle : 0.597 9.667 19399 Z= 0.317 Chirality : 0.041 0.194 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.487 51.574 1992 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.45 % Allowed : 31.06 % Favored : 62.48 % 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: 0.89 (0.19), residues: 1822 helix: 1.23 (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 0.009 0.001 TRP T 208 HIS 0.006 0.001 HIS V 149 PHE 0.023 0.001 PHE Z 123 TYR 0.027 0.002 TYR N 48 ARG 0.005 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 1238) hydrogen bonds : angle 4.02240 ( 3684) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.33476 ( 4) covalent geometry : bond 0.00333 (14321) covalent geometry : angle 0.59690 (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 419 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 1.522 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: 0.8880 (mt0) cc_final: 0.8672 (mt0) REVERT: V 79 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8357 (mm) REVERT: V 130 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7553 (p0) REVERT: V 131 LEU cc_start: 0.8671 (mt) cc_final: 0.8250 (pp) REVERT: X 18 PHE cc_start: 0.9290 (t80) cc_final: 0.8923 (t80) REVERT: X 115 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8657 (tm-30) REVERT: U 34 MET cc_start: 0.8647 (pmm) cc_final: 0.8373 (pmm) REVERT: I 57 GLU cc_start: 0.9415 (tp30) cc_final: 0.9140 (tp30) REVERT: J 61 ILE cc_start: 0.9209 (mm) cc_final: 0.8905 (pt) REVERT: L 33 GLN cc_start: 0.9272 (mt0) cc_final: 0.8985 (mm-40) REVERT: M 41 ILE cc_start: 0.8584 (tp) cc_final: 0.8336 (tt) REVERT: O 49 MET cc_start: 0.9177 (tmm) cc_final: 0.8914 (tmm) REVERT: Q 37 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8429 (mpt-90) REVERT: T 122 TRP cc_start: 0.9307 (m-10) cc_final: 0.8997 (m-10) REVERT: T 294 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9363 (mm) REVERT: Z 85 GLU cc_start: 0.9150 (tt0) cc_final: 0.8823 (tt0) REVERT: Z 92 TYR cc_start: 0.9284 (t80) cc_final: 0.8941 (t80) REVERT: Z 206 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9023 (mm-30) REVERT: Z 267 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8186 (mm) REVERT: Z 280 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8547 (tm-30) outliers start: 91 outliers final: 59 residues processed: 381 average time/residue: 0.2299 time to fit residues: 130.4667 Evaluate side-chains 367 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 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 67 VAL 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: 2.9990 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.096665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075366 restraints weight = 47894.709| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.73 r_work: 0.3283 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14323 Z= 0.157 Angle : 0.598 8.742 19399 Z= 0.316 Chirality : 0.041 0.196 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.295 50.613 1989 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.02 % Allowed : 30.78 % Favored : 62.20 % 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: 0.93 (0.19), residues: 1822 helix: 1.27 (0.13), residues: 1466 sheet: None (None), residues: 0 loop : -2.08 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.006 0.001 HIS V 149 PHE 0.019 0.001 PHE Z 123 TYR 0.023 0.002 TYR N 48 ARG 0.005 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 1238) hydrogen bonds : angle 3.95220 ( 3684) SS BOND : bond 0.00017 ( 2) SS BOND : angle 0.89117 ( 4) covalent geometry : bond 0.00338 (14321) covalent geometry : angle 0.59750 (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: 99 poor density : 326 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 90 GLN cc_start: 0.8910 (mt0) cc_final: 0.8633 (mt0) REVERT: Y 119 ARG cc_start: 0.8784 (tmm160) cc_final: 0.8371 (tmm160) REVERT: V 79 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8373 (mm) REVERT: V 130 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7489 (p0) REVERT: V 131 LEU cc_start: 0.8673 (mt) cc_final: 0.8280 (pp) REVERT: X 18 PHE cc_start: 0.9325 (t80) cc_final: 0.8914 (t80) REVERT: X 74 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8777 (tm-30) REVERT: X 78 LYS cc_start: 0.8109 (pttm) cc_final: 0.7755 (pttm) REVERT: X 115 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8629 (tm-30) REVERT: X 120 MET cc_start: 0.8840 (tpt) cc_final: 0.8628 (tpt) REVERT: U 34 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8413 (pmm) REVERT: U 117 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6667 (ttp80) REVERT: I 57 GLU cc_start: 0.9417 (tp30) cc_final: 0.9174 (tp30) REVERT: L 33 GLN cc_start: 0.9266 (mt0) cc_final: 0.8910 (mm110) REVERT: M 37 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7622 (ttm-80) REVERT: M 41 ILE cc_start: 0.8645 (tp) cc_final: 0.8335 (tt) REVERT: O 1 MET cc_start: 0.6654 (tpt) cc_final: 0.6247 (tpt) REVERT: O 49 MET cc_start: 0.9181 (tmm) cc_final: 0.8827 (tmm) REVERT: P 42 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7996 (pp20) REVERT: T 85 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: T 122 TRP cc_start: 0.9304 (m-10) cc_final: 0.9039 (m-10) REVERT: Z 92 TYR cc_start: 0.9264 (t80) cc_final: 0.8939 (t80) REVERT: Z 267 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8206 (mm) REVERT: Z 280 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8522 (tm-30) outliers start: 99 outliers final: 68 residues processed: 378 average time/residue: 0.2371 time to fit residues: 132.4460 Evaluate side-chains 385 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 41 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 64 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 O residue 65 VAL Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 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 15 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: 1.9990 chunk 177 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** Z 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.096267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074980 restraints weight = 48260.423| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.68 r_work: 0.3271 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1803 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= 0.164 Angle : 0.620 11.533 19399 Z= 0.322 Chirality : 0.042 0.259 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.284 50.767 1989 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 7.59 % Allowed : 31.84 % Favored : 60.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.19), residues: 1822 helix: 1.36 (0.13), residues: 1461 sheet: None (None), residues: 0 loop : -2.08 (0.30), residues: 361 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 0.019 0.001 PHE L 62 TYR 0.021 0.002 TYR N 48 ARG 0.009 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 1238) hydrogen bonds : angle 3.91571 ( 3684) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.79533 ( 4) covalent geometry : bond 0.00355 (14321) covalent geometry : angle 0.62006 (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 421 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 314 time to evaluate : 1.531 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: 0.8784 (tmm160) cc_final: 0.8385 (tmm160) REVERT: V 46 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: V 79 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8357 (mm) REVERT: V 130 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7505 (p0) REVERT: V 131 LEU cc_start: 0.8651 (mt) cc_final: 0.8250 (pp) REVERT: X 18 PHE cc_start: 0.9332 (t80) cc_final: 0.8927 (t80) REVERT: X 115 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8643 (tm-30) REVERT: X 120 MET cc_start: 0.8846 (tpt) cc_final: 0.8607 (tpt) REVERT: U 34 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8401 (pmm) REVERT: U 117 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6647 (ttp80) REVERT: H 43 ASN cc_start: 0.8559 (m110) cc_final: 0.8347 (p0) REVERT: K 1 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7644 (tpp) REVERT: L 33 GLN cc_start: 0.9295 (mt0) cc_final: 0.8931 (mm110) REVERT: M 41 ILE cc_start: 0.8659 (tp) cc_final: 0.8260 (tt) REVERT: M 48 TYR cc_start: 0.8533 (m-10) cc_final: 0.8157 (m-10) REVERT: M 70 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8617 (mp) REVERT: O 1 MET cc_start: 0.6740 (tpt) cc_final: 0.6426 (tpt) REVERT: O 49 MET cc_start: 0.9203 (tmm) cc_final: 0.8813 (tmm) REVERT: P 42 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: T 85 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: T 122 TRP cc_start: 0.9283 (m-10) cc_final: 0.9021 (m-10) REVERT: Z 267 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8361 (mm) REVERT: Z 280 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8531 (tm-30) outliers start: 107 outliers final: 71 residues processed: 372 average time/residue: 0.2436 time to fit residues: 134.1383 Evaluate side-chains 381 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 118 ILE Chi-restraints excluded: chain V residue 127 GLN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 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 133 THR 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 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 45 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain K residue 1 MET 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 53 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 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 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 15 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Z 136 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.096741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075496 restraints weight = 48558.753| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.71 r_work: 0.3289 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14323 Z= 0.152 Angle : 0.617 8.331 19399 Z= 0.323 Chirality : 0.042 0.349 2334 Planarity : 0.005 0.083 2483 Dihedral : 4.288 51.036 1989 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.45 % Allowed : 32.48 % 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: 1.07 (0.19), residues: 1822 helix: 1.38 (0.13), residues: 1463 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 359 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 L 62 TYR 0.021 0.002 TYR Z 92 ARG 0.011 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 1238) hydrogen bonds : angle 3.87904 ( 3684) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.70285 ( 4) covalent geometry : bond 0.00326 (14321) covalent geometry : angle 0.61719 (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 415 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 310 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 119 ARG cc_start: 0.8807 (tmm160) cc_final: 0.8406 (tmm160) REVERT: V 79 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8322 (mm) REVERT: X 18 PHE cc_start: 0.9334 (t80) cc_final: 0.8943 (t80) REVERT: X 74 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8806 (tm-30) REVERT: X 78 LYS cc_start: 0.7932 (pttm) cc_final: 0.7647 (pttm) REVERT: X 115 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8598 (tm-30) REVERT: X 120 MET cc_start: 0.8832 (tpt) cc_final: 0.8558 (tpt) REVERT: U 117 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6643 (ttp80) REVERT: L 33 GLN cc_start: 0.9303 (mt0) cc_final: 0.8944 (mm110) REVERT: L 61 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8432 (mm) REVERT: M 41 ILE cc_start: 0.8666 (tp) cc_final: 0.8237 (tt) REVERT: M 70 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8584 (mp) REVERT: O 1 MET cc_start: 0.6720 (tpt) cc_final: 0.6395 (tpt) REVERT: O 49 MET cc_start: 0.9208 (tmm) cc_final: 0.8936 (tmm) REVERT: P 42 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7956 (pp20) REVERT: T 85 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: T 122 TRP cc_start: 0.9286 (m-10) cc_final: 0.9009 (m-10) REVERT: Z 280 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8596 (tm-30) outliers start: 105 outliers final: 74 residues processed: 367 average time/residue: 0.2322 time to fit residues: 125.6109 Evaluate side-chains 382 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 34 MET 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 127 GLN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 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 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 45 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 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 18 ILE 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 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 61 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 M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 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 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 62 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 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: 3.9990 chunk 75 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN ** Z 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.096775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075609 restraints weight = 48358.589| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.71 r_work: 0.3281 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14323 Z= 0.154 Angle : 0.637 10.114 19399 Z= 0.330 Chirality : 0.041 0.278 2334 Planarity : 0.005 0.082 2483 Dihedral : 4.291 51.358 1989 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.60 % Allowed : 33.40 % Favored : 60.00 % 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: 1.17 (0.19), residues: 1822 helix: 1.42 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.019 0.001 PHE L 62 TYR 0.022 0.002 TYR I 48 ARG 0.012 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 1238) hydrogen bonds : angle 3.86279 ( 3684) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.67723 ( 4) covalent geometry : bond 0.00335 (14321) covalent geometry : angle 0.63744 (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 404 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 311 time to evaluate : 1.493 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: 0.9377 (OUTLIER) cc_final: 0.9049 (mm-40) REVERT: Y 119 ARG cc_start: 0.8809 (tmm160) cc_final: 0.8603 (ttp80) REVERT: V 46 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: V 79 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8406 (mm) REVERT: X 18 PHE cc_start: 0.9337 (t80) cc_final: 0.8897 (t80) REVERT: X 74 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8796 (tm-30) REVERT: X 78 LYS cc_start: 0.7975 (pttm) cc_final: 0.7663 (pttm) REVERT: X 115 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8626 (tm-30) REVERT: X 120 MET cc_start: 0.8852 (tpt) cc_final: 0.8600 (tpt) REVERT: U 117 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6614 (ttp80) REVERT: J 61 ILE cc_start: 0.9158 (mm) cc_final: 0.8923 (pt) REVERT: K 1 MET cc_start: 0.8106 (tpt) cc_final: 0.7349 (tpp) REVERT: L 33 GLN cc_start: 0.9290 (mt0) cc_final: 0.8923 (mm110) REVERT: L 61 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8457 (mm) REVERT: M 41 ILE cc_start: 0.8672 (tp) cc_final: 0.8332 (tt) REVERT: M 70 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8539 (mp) REVERT: O 1 MET cc_start: 0.6741 (tpt) cc_final: 0.6499 (tpt) REVERT: O 49 MET cc_start: 0.9188 (tmm) cc_final: 0.8874 (tmm) REVERT: P 42 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7929 (pp20) REVERT: T 85 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: T 122 TRP cc_start: 0.9278 (m-10) cc_final: 0.9003 (m-10) REVERT: Z 92 TYR cc_start: 0.9295 (t80) cc_final: 0.9036 (t80) REVERT: Z 280 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8605 (tm-30) outliers start: 93 outliers final: 73 residues processed: 362 average time/residue: 0.2404 time to fit residues: 128.6476 Evaluate side-chains 380 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 298 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 74 GLN Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain 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 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 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 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 65 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 11 LEU 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 61 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 195 PHE Chi-restraints excluded: chain T residue 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 62 VAL Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 235 GLU Chi-restraints excluded: chain Z residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 158 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 GLN U 74 GLN L 33 GLN ** Z 121 ASN ** 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 = 0.097940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076874 restraints weight = 48299.850| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.72 r_work: 0.3311 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14323 Z= 0.141 Angle : 0.633 9.394 19399 Z= 0.327 Chirality : 0.041 0.254 2334 Planarity : 0.005 0.081 2483 Dihedral : 4.284 52.108 1989 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.17 % Allowed : 34.04 % 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: 1.45 (0.13), residues: 1473 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 208 HIS 0.003 0.001 HIS V 149 PHE 0.024 0.001 PHE Z 251 TYR 0.019 0.002 TYR P 48 ARG 0.014 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 1238) hydrogen bonds : angle 3.81902 ( 3684) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.63502 ( 4) covalent geometry : bond 0.00297 (14321) covalent geometry : angle 0.63262 (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 398 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 311 time to evaluate : 1.624 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: 0.9387 (OUTLIER) cc_final: 0.8912 (mm-40) REVERT: Y 119 ARG cc_start: 0.8862 (tmm160) cc_final: 0.8649 (ttp80) REVERT: V 79 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8368 (mm) REVERT: X 18 PHE cc_start: 0.9334 (t80) cc_final: 0.8882 (t80) REVERT: X 74 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8765 (tm-30) REVERT: X 78 LYS cc_start: 0.8003 (pttm) cc_final: 0.7699 (pttm) REVERT: X 115 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8645 (tm-30) REVERT: X 120 MET cc_start: 0.8828 (tpt) cc_final: 0.8538 (tpt) REVERT: U 117 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6628 (ttp80) REVERT: J 61 ILE cc_start: 0.9150 (mm) cc_final: 0.8930 (pt) REVERT: K 1 MET cc_start: 0.8046 (tpt) cc_final: 0.7447 (tpp) REVERT: K 2 GLU cc_start: 0.8670 (pm20) cc_final: 0.8398 (pm20) REVERT: L 33 GLN cc_start: 0.9277 (mt0) cc_final: 0.8939 (mm110) REVERT: L 61 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (mm) REVERT: M 41 ILE cc_start: 0.8639 (tp) cc_final: 0.8289 (tt) REVERT: M 70 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8494 (mp) REVERT: O 1 MET cc_start: 0.6600 (tpt) cc_final: 0.6318 (tpt) REVERT: O 49 MET cc_start: 0.9213 (tmm) cc_final: 0.8914 (tmm) REVERT: P 42 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7902 (pp20) REVERT: T 85 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: T 122 TRP cc_start: 0.9248 (m-10) cc_final: 0.8977 (m-10) REVERT: Z 33 GLU cc_start: 0.8233 (mp0) cc_final: 0.8022 (mp0) REVERT: Z 92 TYR cc_start: 0.9205 (t80) cc_final: 0.8962 (t80) REVERT: Z 195 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9154 (t80) REVERT: Z 280 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8607 (tm-30) outliers start: 87 outliers final: 63 residues processed: 363 average time/residue: 0.2330 time to fit residues: 124.9154 Evaluate side-chains 378 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 306 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 X residue 157 LEU Chi-restraints excluded: chain U residue 6 ILE Chi-restraints excluded: chain U residue 23 PHE Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 63 ARG Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 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 68 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 57 GLU 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 45 VAL Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 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: 0.9990 chunk 76 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.097780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076687 restraints weight = 47940.062| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.70 r_work: 0.3314 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14323 Z= 0.145 Angle : 0.660 9.873 19399 Z= 0.337 Chirality : 0.042 0.243 2334 Planarity : 0.005 0.081 2483 Dihedral : 4.252 51.966 1989 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.74 % Allowed : 34.75 % 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: 1469 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.022 0.001 PHE Z 251 TYR 0.022 0.002 TYR I 48 ARG 0.010 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 1238) hydrogen bonds : angle 3.82412 ( 3684) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.60193 ( 4) covalent geometry : bond 0.00315 (14321) covalent geometry : angle 0.66003 (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 392 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 311 time to evaluate : 1.514 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: 0.9396 (OUTLIER) cc_final: 0.8917 (mm-40) REVERT: Y 119 ARG cc_start: 0.8859 (tmm160) cc_final: 0.8605 (ttp80) REVERT: V 46 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: V 79 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8374 (mm) REVERT: X 18 PHE cc_start: 0.9329 (t80) cc_final: 0.8869 (t80) REVERT: X 74 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: X 78 LYS cc_start: 0.8007 (pttm) cc_final: 0.7693 (pttm) REVERT: X 115 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8633 (tm-30) REVERT: X 120 MET cc_start: 0.8884 (tpt) cc_final: 0.8624 (tpt) REVERT: U 108 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8763 (mp0) REVERT: U 117 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6645 (ttp80) REVERT: I 1 MET cc_start: 0.6984 (mmm) cc_final: 0.6702 (mmm) REVERT: J 61 ILE cc_start: 0.9134 (mm) cc_final: 0.8924 (pt) REVERT: K 1 MET cc_start: 0.8008 (tpt) cc_final: 0.7413 (tpp) REVERT: K 2 GLU cc_start: 0.8582 (pm20) cc_final: 0.8343 (pm20) REVERT: L 33 GLN cc_start: 0.9267 (mt0) cc_final: 0.8777 (tm-30) REVERT: L 61 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8410 (mm) REVERT: M 41 ILE cc_start: 0.8621 (tp) cc_final: 0.8263 (tt) REVERT: M 70 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8535 (mp) REVERT: O 1 MET cc_start: 0.6670 (tpt) cc_final: 0.6398 (tpt) REVERT: O 49 MET cc_start: 0.9218 (tmm) cc_final: 0.8920 (tmm) REVERT: P 42 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: T 85 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: T 122 TRP cc_start: 0.9253 (m-10) cc_final: 0.8982 (m-10) REVERT: T 242 LYS cc_start: 0.9381 (mmtp) cc_final: 0.8965 (mmtp) REVERT: Z 195 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.9097 (t80) REVERT: Z 280 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8625 (tm-30) outliers start: 81 outliers final: 65 residues processed: 358 average time/residue: 0.2640 time to fit residues: 144.0122 Evaluate side-chains 379 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 304 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 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 74 GLN Chi-restraints excluded: chain X residue 104 ARG Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain U residue 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 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 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 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 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 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 175 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 162 optimal weight: 0.0030 chunk 104 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 0.0170 overall best weight: 0.4028 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.098449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077470 restraints weight = 48463.594| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.73 r_work: 0.3336 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 14323 Z= 0.144 Angle : 0.671 9.705 19399 Z= 0.340 Chirality : 0.042 0.274 2334 Planarity : 0.005 0.080 2483 Dihedral : 4.254 52.273 1989 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.11 % Allowed : 35.32 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1822 helix: 1.51 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -2.10 (0.30), 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 0.021 0.001 PHE Z 251 TYR 0.018 0.002 TYR P 48 ARG 0.018 0.000 ARG V 86 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1238) hydrogen bonds : angle 3.82438 ( 3684) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.57744 ( 4) covalent geometry : bond 0.00312 (14321) covalent geometry : angle 0.67060 (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 391 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 319 time to evaluate : 1.733 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: 0.9420 (OUTLIER) cc_final: 0.8946 (mm-40) REVERT: Y 119 ARG cc_start: 0.8859 (tmm160) cc_final: 0.8638 (ttp80) REVERT: V 79 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8365 (mm) REVERT: X 18 PHE cc_start: 0.9336 (t80) cc_final: 0.8879 (t80) REVERT: X 74 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8793 (tm-30) REVERT: X 78 LYS cc_start: 0.7973 (pttm) cc_final: 0.7703 (pttm) REVERT: X 115 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8620 (tm-30) REVERT: X 120 MET cc_start: 0.8851 (tpt) cc_final: 0.8611 (tpt) REVERT: U 108 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8737 (mp0) REVERT: U 117 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6713 (ttp80) REVERT: I 1 MET cc_start: 0.6891 (mmm) cc_final: 0.6577 (mmm) REVERT: K 1 MET cc_start: 0.8049 (tpt) cc_final: 0.7588 (tpp) REVERT: K 2 GLU cc_start: 0.8559 (pm20) cc_final: 0.8336 (pm20) REVERT: L 33 GLN cc_start: 0.9275 (mt0) cc_final: 0.8766 (tm-30) REVERT: L 61 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8448 (mm) REVERT: M 41 ILE cc_start: 0.8599 (tp) cc_final: 0.8237 (tt) REVERT: M 70 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8614 (mp) REVERT: O 1 MET cc_start: 0.6610 (tpt) cc_final: 0.6346 (tpt) REVERT: O 49 MET cc_start: 0.9227 (tmm) cc_final: 0.8927 (tmm) REVERT: P 42 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7915 (pp20) REVERT: Q 48 TYR cc_start: 0.9071 (m-10) cc_final: 0.8844 (m-80) REVERT: T 22 ARG cc_start: 0.6536 (ptt-90) cc_final: 0.5980 (ptp90) REVERT: T 85 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: T 122 TRP cc_start: 0.9256 (m-10) cc_final: 0.8771 (m100) REVERT: Z 195 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9091 (t80) REVERT: Z 280 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 72 outliers final: 59 residues processed: 362 average time/residue: 0.2329 time to fit residues: 125.7505 Evaluate side-chains 377 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 117 ARG Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 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 L residue 7 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 23 PHE Chi-restraints excluded: chain T residue 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 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: 7.9990 chunk 154 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 133 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** U 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.098153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077108 restraints weight = 48716.683| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.74 r_work: 0.3326 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 0.091 14323 Z= 0.151 Angle : 0.701 12.957 19399 Z= 0.356 Chirality : 0.043 0.264 2334 Planarity : 0.005 0.080 2483 Dihedral : 4.264 52.541 1989 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.39 % Allowed : 35.74 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1467 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.003 0.000 HIS V 149 PHE 0.020 0.001 PHE Z 251 TYR 0.024 0.002 TYR I 48 ARG 0.004 0.000 ARG X 86 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 1238) hydrogen bonds : angle 3.84678 ( 3684) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.55200 ( 4) covalent geometry : bond 0.00337 (14321) covalent geometry : angle 0.70147 (19395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7369.44 seconds wall clock time: 128 minutes 2.08 seconds (7682.08 seconds total)