Starting phenix.real_space_refine on Thu May 15 07:25:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itw_60881/05_2025/9itw_60881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itw_60881/05_2025/9itw_60881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itw_60881/05_2025/9itw_60881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itw_60881/05_2025/9itw_60881.map" model { file = "/net/cci-nas-00/data/ceres_data/9itw_60881/05_2025/9itw_60881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itw_60881/05_2025/9itw_60881.cif" } resolution = 4.08 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= 0.009 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 33 5.16 5 C 8456 2.51 5 N 2219 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 12998 Number of models: 1 Model: "" Number of chains: 16 Chain: "Y" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1223 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} 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: "U" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 772 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 292 Chain: "X" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 820 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 1, 'TRANS': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 20, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 259 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: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} 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: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "O" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "P" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Q" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "T" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1865 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Chain: "Z" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1941 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 8.83, per 1000 atoms: 0.68 Number of scatterers: 12998 At special positions: 0 Unit cell: (87.42, 142.29, 225.99, 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 33 16.00 O 2290 8.00 N 2219 7.00 C 8456 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=2.89 Simple disulfide: pdb=" SG CYS Z 135 " - pdb=" SG CYS Z 173 " distance=2.63 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: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'Y' and resid 8 through 147 removed outlier: 3.912A pdb=" N ILE Y 12 " --> pdb=" O PRO Y 8 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR Y 30 " --> pdb=" O ARG Y 26 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix removed outlier: 3.505A pdb=" N GLN Y 89 " --> pdb=" O GLU Y 85 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA Y 146 " --> pdb=" O ALA Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 159 Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 113 Processing helix chain 'V' and resid 115 through 120 Processing helix chain 'V' and resid 122 through 137 removed outlier: 4.277A pdb=" N ILE V 128 " --> pdb=" O ALA V 124 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA V 129 " --> pdb=" O LYS V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 157 removed outlier: 3.834A pdb=" N LEU V 152 " --> pdb=" O GLY V 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 120 removed outlier: 3.535A pdb=" N PHE U 11 " --> pdb=" O ASN U 7 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG U 26 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA U 27 " --> pdb=" O PHE U 23 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR U 30 " --> pdb=" O ARG U 26 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.707A pdb=" N GLU U 39 " --> pdb=" O ASN U 35 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG U 63 " --> pdb=" O ALA U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 140 removed outlier: 3.685A pdb=" N ALA U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS U 125 " --> pdb=" O LEU U 121 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER U 126 " --> pdb=" O SER U 122 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA U 136 " --> pdb=" O VAL U 132 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER U 137 " --> pdb=" O THR U 133 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG U 138 " --> pdb=" O LEU U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 159 Processing helix chain 'X' and resid 11 through 29 removed outlier: 3.633A pdb=" N ASN X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 122 removed outlier: 3.568A pdb=" N LEU X 37 " --> pdb=" O VAL X 33 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG X 49 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU X 75 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE X 95 " --> pdb=" O GLU X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.685A pdb=" N SER X 126 " --> pdb=" O SER X 122 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN X 127 " --> pdb=" O GLU X 123 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE X 128 " --> pdb=" O ALA X 124 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP X 130 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU X 131 " --> pdb=" O GLN X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 135 through 142 Processing helix chain 'X' and resid 142 through 147 removed outlier: 3.650A pdb=" N ALA X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 160 Processing helix chain 'H' and resid 3 through 38 removed outlier: 4.426A 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 72 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 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 72 Processing helix chain 'K' and resid 3 through 38 removed outlier: 4.214A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 Processing helix chain 'L' and resid 3 through 17 removed outlier: 3.534A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 37 removed outlier: 3.871A 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 72 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: 4.275A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 38 removed outlier: 4.055A 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 Processing helix chain 'O' and resid 5 through 38 Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 41 through 73 removed outlier: 4.141A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 37 Proline residue: P 20 - end of helix removed outlier: 3.854A pdb=" N ARG P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 71 removed outlier: 4.178A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.565A 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: 4.535A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.619A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.821A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.553A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 178 removed outlier: 4.276A pdb=" N ALA T 175 " --> pdb=" O THR T 172 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN T 176 " --> pdb=" O CYS T 173 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY T 177 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.548A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 212 removed outlier: 3.993A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 215 No H-bonds generated for 'chain 'T' and resid 213 through 215' Processing helix chain 'T' and resid 216 through 221 Processing helix chain 'T' and resid 227 through 268 removed outlier: 3.566A pdb=" N ILE T 233 " --> pdb=" O SER T 229 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE T 234 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.911A pdb=" N PHE T 285 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 21 removed outlier: 3.720A pdb=" N ALA Z 20 " --> pdb=" O ILE Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 71 Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.745A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.611A pdb=" N VAL Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 176 Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.649A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Z 212 " --> pdb=" O TRP Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 219 removed outlier: 3.650A pdb=" N LEU Z 218 " --> pdb=" O GLY Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 225 removed outlier: 3.830A pdb=" N ASN Z 225 " --> pdb=" O PHE Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 268 removed outlier: 3.588A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 3.568A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 4.739A pdb=" N PHE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3831 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: 3.81 Time building geometry restraints manager: 3.71 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: 4106 1.34 - 1.46: 1512 1.46 - 1.57: 7500 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 13180 Sorted by residual: bond pdb=" N ILE T 39 " pdb=" CA ILE T 39 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.19e-02 7.06e+03 9.82e+00 bond pdb=" N ILE U 44 " pdb=" CA ILE U 44 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" C ALA X 142 " pdb=" O ALA X 142 " ideal model delta sigma weight residual 1.234 1.272 -0.038 1.30e-02 5.92e+03 8.54e+00 bond pdb=" N LEU U 37 " pdb=" CA LEU U 37 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.53e+00 bond pdb=" N VAL T 303 " pdb=" CA VAL T 303 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.30e-02 5.92e+03 8.37e+00 ... (remaining 13175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 17239 1.63 - 3.26: 618 3.26 - 4.89: 62 4.89 - 6.53: 19 6.53 - 8.16: 4 Bond angle restraints: 17942 Sorted by residual: angle pdb=" N THR X 135 " pdb=" CA THR X 135 " pdb=" C THR X 135 " ideal model delta sigma weight residual 113.17 105.01 8.16 1.26e+00 6.30e-01 4.19e+01 angle pdb=" N VAL X 48 " pdb=" CA VAL X 48 " pdb=" C VAL X 48 " ideal model delta sigma weight residual 110.72 104.35 6.37 1.01e+00 9.80e-01 3.98e+01 angle pdb=" N ILE O 41 " pdb=" CA ILE O 41 " pdb=" C ILE O 41 " ideal model delta sigma weight residual 111.91 107.20 4.71 8.90e-01 1.26e+00 2.80e+01 angle pdb=" N ILE I 41 " pdb=" CA ILE I 41 " pdb=" C ILE I 41 " ideal model delta sigma weight residual 111.91 107.63 4.28 8.90e-01 1.26e+00 2.31e+01 angle pdb=" O GLN U 115 " pdb=" C GLN U 115 " pdb=" N GLU U 116 " ideal model delta sigma weight residual 122.07 126.36 -4.29 1.03e+00 9.43e-01 1.74e+01 ... (remaining 17937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7079 17.86 - 35.72: 518 35.72 - 53.58: 73 53.58 - 71.44: 11 71.44 - 89.30: 13 Dihedral angle restraints: 7694 sinusoidal: 2440 harmonic: 5254 Sorted by residual: 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 -86.00 -172.29 86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CG ARG Y 86 " pdb=" CD ARG Y 86 " pdb=" NE ARG Y 86 " pdb=" CZ ARG Y 86 " ideal model delta sinusoidal sigma weight residual -90.00 -134.55 44.55 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU V 114 " pdb=" CG GLU V 114 " pdb=" CD GLU V 114 " pdb=" OE1 GLU V 114 " ideal model delta sinusoidal sigma weight residual 0.00 -88.64 88.64 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1816 0.057 - 0.114: 335 0.114 - 0.171: 57 0.171 - 0.228: 13 0.228 - 0.285: 5 Chirality restraints: 2226 Sorted by residual: chirality pdb=" CG LEU Z 261 " pdb=" CB LEU Z 261 " pdb=" CD1 LEU Z 261 " pdb=" CD2 LEU Z 261 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE H 41 " pdb=" CA ILE H 41 " pdb=" CG1 ILE H 41 " pdb=" CG2 ILE H 41 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL X 48 " pdb=" N VAL X 48 " pdb=" C VAL X 48 " pdb=" CB VAL X 48 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2223 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO Q 20 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 46 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C GLU X 46 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU X 46 " 0.016 2.00e-02 2.50e+03 pdb=" N SER X 47 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY M 19 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO M 20 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO M 20 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 20 " -0.031 5.00e-02 4.00e+02 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4301 2.84 - 3.35: 14663 3.35 - 3.87: 22083 3.87 - 4.38: 24138 4.38 - 4.90: 41098 Nonbonded interactions: 106283 Sorted by model distance: nonbonded pdb=" O ILE Y 44 " pdb=" OG SER Y 47 " model vdw 2.321 3.040 nonbonded pdb=" O ARG I 44 " pdb=" OG1 THR I 47 " model vdw 2.363 3.040 nonbonded pdb=" O ASN T 99 " pdb=" OH TYR T 296 " model vdw 2.366 3.040 nonbonded pdb=" NH2 ARG Y 138 " pdb=" OG SER V 156 " model vdw 2.368 3.120 nonbonded pdb=" O ALA X 13 " pdb=" ND2 ASN X 17 " model vdw 2.374 3.120 ... (remaining 106278 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 78 and (name N or name CA or name C or name O \ or name CB )) or resid 79 or (resid 80 through 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 304)) } ncs_group { reference = (chain 'U' and resid 10 through 158) selection = (chain 'V' and ((resid 10 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or nam \ e O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'X' and ((resid 10 through 140 and (name N or name CA or name C or name O \ or name CB )) or resid 141 through 158)) selection = (chain 'Y' and ((resid 10 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or nam \ e O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA \ or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.950 Find NCS groups from input model: 0.650 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.010 0.858 13182 Z= 0.546 Angle : 0.695 15.873 17946 Z= 0.473 Chirality : 0.047 0.285 2226 Planarity : 0.005 0.066 2320 Dihedral : 13.282 89.299 4308 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.37 (0.19), residues: 1830 helix: 1.47 (0.12), residues: 1516 sheet: None (None), residues: 0 loop : -1.78 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.028 0.001 PHE T 222 TYR 0.023 0.001 TYR T 92 ARG 0.004 0.000 ARG Y 138 Details of bonding type rmsd hydrogen bonds : bond 0.14716 ( 1284) hydrogen bonds : angle 5.13594 ( 3831) SS BOND : bond 0.74086 ( 2) SS BOND : angle 8.35350 ( 4) covalent geometry : bond 0.00446 (13180) covalent geometry : angle 0.68332 (17942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 LEU cc_start: 0.9701 (mt) cc_final: 0.9493 (tt) REVERT: Y 33 VAL cc_start: 0.9561 (t) cc_final: 0.9249 (p) REVERT: Y 85 GLU cc_start: 0.8913 (tt0) cc_final: 0.8673 (tm-30) REVERT: V 34 MET cc_start: 0.9038 (tpt) cc_final: 0.8815 (tmm) REVERT: V 103 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8641 (tp30) REVERT: H 7 VAL cc_start: 0.9407 (t) cc_final: 0.9076 (p) REVERT: H 11 LEU cc_start: 0.9526 (mt) cc_final: 0.9254 (mp) REVERT: H 20 PRO cc_start: 0.8488 (Cg_exo) cc_final: 0.7929 (Cg_endo) REVERT: H 43 ASN cc_start: 0.8651 (p0) cc_final: 0.8305 (p0) REVERT: H 48 TYR cc_start: 0.8816 (m-80) cc_final: 0.8275 (m-80) REVERT: H 55 PHE cc_start: 0.9081 (m-80) cc_final: 0.8657 (m-80) REVERT: H 56 THR cc_start: 0.9312 (p) cc_final: 0.8914 (p) REVERT: H 66 ILE cc_start: 0.9464 (tt) cc_final: 0.9235 (mm) REVERT: I 48 TYR cc_start: 0.9061 (m-80) cc_final: 0.8255 (m-80) REVERT: I 49 MET cc_start: 0.9152 (ttp) cc_final: 0.8704 (tmm) REVERT: I 51 ILE cc_start: 0.9453 (mt) cc_final: 0.9251 (tp) REVERT: I 55 PHE cc_start: 0.9041 (m-10) cc_final: 0.8716 (m-10) REVERT: J 49 MET cc_start: 0.9379 (ttp) cc_final: 0.9034 (tmm) REVERT: K 48 TYR cc_start: 0.9136 (m-10) cc_final: 0.8286 (m-80) REVERT: K 53 ILE cc_start: 0.9565 (mt) cc_final: 0.9364 (mm) REVERT: K 57 GLU cc_start: 0.9432 (tp30) cc_final: 0.8914 (pt0) REVERT: K 66 ILE cc_start: 0.9241 (tt) cc_final: 0.9014 (tt) REVERT: L 15 LEU cc_start: 0.9246 (mt) cc_final: 0.8927 (tp) REVERT: L 20 PRO cc_start: 0.9087 (Cg_exo) cc_final: 0.8637 (Cg_endo) REVERT: L 22 VAL cc_start: 0.9430 (t) cc_final: 0.9193 (m) REVERT: L 24 ILE cc_start: 0.9452 (mt) cc_final: 0.9075 (mt) REVERT: L 29 SER cc_start: 0.9673 (t) cc_final: 0.9263 (m) REVERT: L 33 GLN cc_start: 0.9469 (tt0) cc_final: 0.9139 (mm110) REVERT: L 35 ILE cc_start: 0.8727 (tt) cc_final: 0.8480 (tp) REVERT: L 48 TYR cc_start: 0.8821 (m-80) cc_final: 0.7811 (m-80) REVERT: L 49 MET cc_start: 0.9211 (tmm) cc_final: 0.8757 (tmm) REVERT: L 57 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8447 (pt0) REVERT: M 11 LEU cc_start: 0.9265 (mt) cc_final: 0.8912 (pp) REVERT: M 24 ILE cc_start: 0.9362 (mt) cc_final: 0.9092 (pt) REVERT: M 26 ILE cc_start: 0.9697 (mt) cc_final: 0.9485 (tt) REVERT: M 41 ILE cc_start: 0.8780 (tp) cc_final: 0.8400 (tp) REVERT: N 51 ILE cc_start: 0.9397 (mt) cc_final: 0.9040 (tt) REVERT: N 53 ILE cc_start: 0.9579 (tt) cc_final: 0.9246 (tt) REVERT: N 55 PHE cc_start: 0.9314 (m-10) cc_final: 0.9074 (m-80) REVERT: N 62 PHE cc_start: 0.9387 (m-10) cc_final: 0.9168 (m-80) REVERT: N 66 ILE cc_start: 0.9359 (mm) cc_final: 0.9055 (mm) REVERT: O 49 MET cc_start: 0.9368 (ttp) cc_final: 0.9091 (tmm) REVERT: O 57 GLU cc_start: 0.9350 (tp30) cc_final: 0.8861 (tp30) REVERT: O 59 LEU cc_start: 0.9509 (mt) cc_final: 0.9308 (mp) REVERT: O 62 PHE cc_start: 0.9358 (m-10) cc_final: 0.9152 (m-80) REVERT: P 1 MET cc_start: 0.6289 (mtt) cc_final: 0.5739 (mtt) REVERT: P 11 LEU cc_start: 0.9468 (mt) cc_final: 0.9175 (mt) REVERT: P 20 PRO cc_start: 0.9469 (Cg_exo) cc_final: 0.9182 (Cg_endo) REVERT: P 33 GLN cc_start: 0.9433 (mt0) cc_final: 0.8867 (mm-40) REVERT: P 57 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9323 (mm-30) REVERT: Q 18 ILE cc_start: 0.9025 (mt) cc_final: 0.8807 (mt) REVERT: Q 20 PRO cc_start: 0.9352 (Cg_exo) cc_final: 0.9051 (Cg_endo) REVERT: Q 50 PHE cc_start: 0.9436 (m-80) cc_final: 0.9200 (m-80) REVERT: Q 68 PHE cc_start: 0.9151 (m-80) cc_final: 0.8746 (m-80) REVERT: T 235 GLU cc_start: 0.9454 (tt0) cc_final: 0.8602 (tp30) REVERT: T 236 PHE cc_start: 0.8830 (t80) cc_final: 0.8327 (t80) REVERT: T 244 PHE cc_start: 0.9140 (m-80) cc_final: 0.8723 (m-80) REVERT: T 264 MET cc_start: 0.9063 (mmt) cc_final: 0.8572 (tpp) REVERT: T 273 PRO cc_start: 0.6240 (Cg_exo) cc_final: 0.4916 (Cg_exo) REVERT: Z 90 SER cc_start: 0.9407 (m) cc_final: 0.9058 (t) REVERT: Z 191 LEU cc_start: 0.9469 (mt) cc_final: 0.9139 (mp) REVERT: Z 206 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8840 (mm-30) REVERT: Z 219 LYS cc_start: 0.4845 (mttp) cc_final: 0.4307 (tttt) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.2137 time to fit residues: 161.0810 Evaluate side-chains 352 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.0270 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 38 ASN V 127 GLN V 149 HIS ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN M 43 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 253 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063671 restraints weight = 84840.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064967 restraints weight = 59079.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.065813 restraints weight = 45199.526| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13182 Z= 0.155 Angle : 0.583 7.596 17946 Z= 0.312 Chirality : 0.041 0.215 2226 Planarity : 0.005 0.058 2320 Dihedral : 3.839 17.361 1945 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.72 % 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: 1.69 (0.19), residues: 1830 helix: 1.70 (0.12), residues: 1517 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.002 0.001 HIS T 136 PHE 0.034 0.002 PHE I 62 TYR 0.008 0.001 TYR L 48 ARG 0.012 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1284) hydrogen bonds : angle 4.03938 ( 3831) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.47839 ( 4) covalent geometry : bond 0.00321 (13180) covalent geometry : angle 0.58332 (17942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 424 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 LEU cc_start: 0.9736 (mt) cc_final: 0.9529 (tt) REVERT: Y 33 VAL cc_start: 0.9556 (t) cc_final: 0.9285 (p) REVERT: Y 34 MET cc_start: 0.9122 (mmp) cc_final: 0.8589 (mmm) REVERT: Y 120 MET cc_start: 0.7499 (tpt) cc_final: 0.7232 (tpt) REVERT: V 34 MET cc_start: 0.9012 (tpt) cc_final: 0.8631 (tmm) REVERT: V 38 ASN cc_start: 0.9262 (m-40) cc_final: 0.8688 (m-40) REVERT: V 89 GLN cc_start: 0.9445 (pt0) cc_final: 0.9166 (pp30) REVERT: H 51 ILE cc_start: 0.9416 (mt) cc_final: 0.8856 (tt) REVERT: H 53 ILE cc_start: 0.9010 (tp) cc_final: 0.8605 (tp) REVERT: H 55 PHE cc_start: 0.9008 (m-80) cc_final: 0.8693 (m-80) REVERT: H 57 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8712 (pt0) REVERT: I 29 SER cc_start: 0.9207 (t) cc_final: 0.8958 (m) REVERT: I 48 TYR cc_start: 0.9044 (m-80) cc_final: 0.8187 (m-80) REVERT: I 49 MET cc_start: 0.9239 (ttp) cc_final: 0.8668 (tmm) REVERT: I 55 PHE cc_start: 0.8987 (m-10) cc_final: 0.8572 (m-10) REVERT: J 15 LEU cc_start: 0.9278 (mt) cc_final: 0.9011 (mp) REVERT: K 48 TYR cc_start: 0.9162 (m-10) cc_final: 0.8533 (m-80) REVERT: K 57 GLU cc_start: 0.9400 (tp30) cc_final: 0.8735 (pt0) REVERT: L 15 LEU cc_start: 0.9159 (mt) cc_final: 0.8846 (tp) REVERT: L 24 ILE cc_start: 0.9405 (mt) cc_final: 0.9077 (mm) REVERT: L 26 ILE cc_start: 0.9792 (mt) cc_final: 0.9533 (mt) REVERT: L 29 SER cc_start: 0.9629 (t) cc_final: 0.9343 (p) REVERT: L 33 GLN cc_start: 0.9427 (tt0) cc_final: 0.9142 (mm110) REVERT: L 48 TYR cc_start: 0.8849 (m-80) cc_final: 0.8020 (m-80) REVERT: L 57 GLU cc_start: 0.9418 (mm-30) cc_final: 0.8334 (pt0) REVERT: L 62 PHE cc_start: 0.8697 (m-10) cc_final: 0.8369 (m-80) REVERT: M 66 ILE cc_start: 0.8990 (mm) cc_final: 0.8745 (mm) REVERT: N 43 ASN cc_start: 0.8814 (p0) cc_final: 0.8593 (p0) REVERT: N 51 ILE cc_start: 0.9369 (mt) cc_final: 0.9076 (tt) REVERT: N 55 PHE cc_start: 0.9400 (m-10) cc_final: 0.9102 (m-80) REVERT: N 57 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8022 (pt0) REVERT: N 59 LEU cc_start: 0.9380 (mm) cc_final: 0.9142 (mm) REVERT: N 62 PHE cc_start: 0.9369 (m-10) cc_final: 0.9045 (m-80) REVERT: N 66 ILE cc_start: 0.9339 (mm) cc_final: 0.9085 (mm) REVERT: O 1 MET cc_start: 0.6868 (tpt) cc_final: 0.6556 (tpt) REVERT: O 57 GLU cc_start: 0.9483 (tp30) cc_final: 0.8964 (tp30) REVERT: O 59 LEU cc_start: 0.9532 (mt) cc_final: 0.9289 (mp) REVERT: O 62 PHE cc_start: 0.9389 (m-10) cc_final: 0.9188 (m-80) REVERT: P 20 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.9071 (Cg_endo) REVERT: P 24 ILE cc_start: 0.9480 (mt) cc_final: 0.9181 (mt) REVERT: P 27 ILE cc_start: 0.9462 (mt) cc_final: 0.9199 (mt) REVERT: P 33 GLN cc_start: 0.9565 (mt0) cc_final: 0.9082 (mm-40) REVERT: P 53 ILE cc_start: 0.9399 (pt) cc_final: 0.8866 (pt) REVERT: P 56 THR cc_start: 0.9087 (p) cc_final: 0.8221 (p) REVERT: P 57 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9103 (mm-30) REVERT: P 59 LEU cc_start: 0.9439 (mm) cc_final: 0.9133 (mm) REVERT: P 62 PHE cc_start: 0.9124 (m-10) cc_final: 0.8847 (m-80) REVERT: P 64 LEU cc_start: 0.9716 (mt) cc_final: 0.9436 (mt) REVERT: Q 1 MET cc_start: 0.6394 (mmm) cc_final: 0.6036 (mmm) REVERT: Q 68 PHE cc_start: 0.9069 (m-80) cc_final: 0.8732 (m-80) REVERT: T 244 PHE cc_start: 0.9141 (m-80) cc_final: 0.8732 (m-80) REVERT: T 264 MET cc_start: 0.9083 (mmt) cc_final: 0.8704 (tpp) REVERT: T 269 PRO cc_start: -0.3996 (Cg_endo) cc_final: -0.4268 (Cg_exo) REVERT: T 273 PRO cc_start: 0.5726 (Cg_exo) cc_final: 0.4739 (Cg_exo) REVERT: Z 89 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8036 (tm-30) REVERT: Z 125 LEU cc_start: 0.9189 (mp) cc_final: 0.8102 (mp) REVERT: Z 206 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8932 (mm-30) REVERT: Z 280 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8835 (tm-30) REVERT: Z 281 VAL cc_start: 0.9480 (p) cc_final: 0.8972 (p) outliers start: 2 outliers final: 1 residues processed: 424 average time/residue: 0.1929 time to fit residues: 124.0103 Evaluate side-chains 350 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 157 optimal weight: 0.0670 chunk 162 optimal weight: 0.0020 chunk 166 optimal weight: 0.8980 overall best weight: 0.5930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 149 HIS ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.080224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063282 restraints weight = 83795.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064595 restraints weight = 58449.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.065464 restraints weight = 45000.440| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13182 Z= 0.144 Angle : 0.577 9.941 17946 Z= 0.307 Chirality : 0.041 0.200 2226 Planarity : 0.004 0.053 2320 Dihedral : 3.787 17.869 1945 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.36 % Allowed : 3.10 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.19), residues: 1830 helix: 1.66 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.023 0.001 PHE Q 50 TYR 0.014 0.001 TYR H 48 ARG 0.005 0.000 ARG Y 73 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 1284) hydrogen bonds : angle 3.84884 ( 3831) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.31611 ( 4) covalent geometry : bond 0.00300 (13180) covalent geometry : angle 0.57723 (17942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 402 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 VAL cc_start: 0.9554 (t) cc_final: 0.9303 (p) REVERT: Y 34 MET cc_start: 0.9103 (mmp) cc_final: 0.8607 (mmm) REVERT: Y 90 GLN cc_start: 0.9025 (mp10) cc_final: 0.8761 (mp10) REVERT: Y 119 ARG cc_start: 0.9610 (mtt180) cc_final: 0.9406 (ptp-110) REVERT: Y 132 VAL cc_start: 0.9557 (p) cc_final: 0.9346 (m) REVERT: V 25 LEU cc_start: 0.9609 (mt) cc_final: 0.9364 (mt) REVERT: V 34 MET cc_start: 0.9003 (tpt) cc_final: 0.8570 (tmm) REVERT: V 38 ASN cc_start: 0.9275 (m-40) cc_final: 0.8705 (m110) REVERT: H 50 PHE cc_start: 0.8949 (m-80) cc_final: 0.8617 (m-10) REVERT: H 51 ILE cc_start: 0.9428 (mt) cc_final: 0.9143 (mt) REVERT: H 53 ILE cc_start: 0.9100 (tp) cc_final: 0.8627 (tp) REVERT: H 57 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8455 (pt0) REVERT: I 29 SER cc_start: 0.9245 (t) cc_final: 0.9025 (p) REVERT: I 48 TYR cc_start: 0.8930 (m-80) cc_final: 0.8141 (m-80) REVERT: I 49 MET cc_start: 0.9147 (ttp) cc_final: 0.8706 (tmm) REVERT: J 35 ILE cc_start: 0.8771 (mm) cc_final: 0.8478 (tp) REVERT: K 1 MET cc_start: 0.6373 (tpp) cc_final: 0.5986 (tpp) REVERT: K 20 PRO cc_start: 0.9434 (Cg_exo) cc_final: 0.9180 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9160 (m-10) cc_final: 0.8624 (m-80) REVERT: K 53 ILE cc_start: 0.9463 (mm) cc_final: 0.9203 (mm) REVERT: K 57 GLU cc_start: 0.9360 (tp30) cc_final: 0.8814 (pt0) REVERT: L 15 LEU cc_start: 0.9193 (mt) cc_final: 0.8945 (tp) REVERT: L 24 ILE cc_start: 0.9403 (mt) cc_final: 0.9131 (mm) REVERT: L 26 ILE cc_start: 0.9770 (mt) cc_final: 0.9466 (tt) REVERT: L 29 SER cc_start: 0.9613 (t) cc_final: 0.9260 (p) REVERT: L 33 GLN cc_start: 0.9448 (tt0) cc_final: 0.9147 (mm110) REVERT: L 41 ILE cc_start: 0.8942 (tp) cc_final: 0.8731 (tp) REVERT: L 48 TYR cc_start: 0.8866 (m-80) cc_final: 0.7847 (m-80) REVERT: L 49 MET cc_start: 0.9410 (ppp) cc_final: 0.9175 (tmm) REVERT: L 57 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8316 (pt0) REVERT: L 62 PHE cc_start: 0.8749 (m-10) cc_final: 0.8473 (m-80) REVERT: M 41 ILE cc_start: 0.8753 (tp) cc_final: 0.8265 (tt) REVERT: N 43 ASN cc_start: 0.8978 (p0) cc_final: 0.8706 (p0) REVERT: N 51 ILE cc_start: 0.9457 (mt) cc_final: 0.9079 (tt) REVERT: N 55 PHE cc_start: 0.9401 (m-10) cc_final: 0.9102 (m-80) REVERT: N 64 LEU cc_start: 0.9394 (mt) cc_final: 0.9026 (mt) REVERT: N 66 ILE cc_start: 0.9314 (mm) cc_final: 0.9045 (mm) REVERT: O 57 GLU cc_start: 0.9458 (tp30) cc_final: 0.8909 (tp30) REVERT: O 59 LEU cc_start: 0.9554 (mt) cc_final: 0.9347 (mp) REVERT: O 62 PHE cc_start: 0.9356 (m-10) cc_final: 0.9144 (m-80) REVERT: P 11 LEU cc_start: 0.9562 (mm) cc_final: 0.9289 (mm) REVERT: P 20 PRO cc_start: 0.9283 (Cg_exo) cc_final: 0.9073 (Cg_endo) REVERT: P 33 GLN cc_start: 0.9561 (mt0) cc_final: 0.9078 (mm-40) REVERT: P 57 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9286 (mm-30) REVERT: P 59 LEU cc_start: 0.9470 (mm) cc_final: 0.9175 (mm) REVERT: P 68 PHE cc_start: 0.9176 (m-80) cc_final: 0.8957 (m-80) REVERT: Q 1 MET cc_start: 0.6509 (mmm) cc_final: 0.5963 (mmm) REVERT: Q 50 PHE cc_start: 0.9370 (m-80) cc_final: 0.9001 (m-80) REVERT: Q 55 PHE cc_start: 0.9054 (m-10) cc_final: 0.8832 (m-80) REVERT: Q 68 PHE cc_start: 0.8950 (m-80) cc_final: 0.8684 (m-80) REVERT: T 244 PHE cc_start: 0.9106 (m-80) cc_final: 0.8779 (m-80) REVERT: T 264 MET cc_start: 0.9014 (mmt) cc_final: 0.8690 (tpp) REVERT: T 273 PRO cc_start: 0.6013 (Cg_exo) cc_final: 0.5499 (Cg_exo) REVERT: Z 89 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7914 (tm-30) REVERT: Z 125 LEU cc_start: 0.9139 (mp) cc_final: 0.7919 (mp) REVERT: Z 206 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8900 (mm-30) REVERT: Z 280 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8728 (tm-30) REVERT: Z 281 VAL cc_start: 0.9420 (p) cc_final: 0.8939 (p) outliers start: 4 outliers final: 2 residues processed: 405 average time/residue: 0.2012 time to fit residues: 123.1170 Evaluate side-chains 340 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 50 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 115 GLN V 115 GLN V 149 HIS ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 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 = 0.3811 r_free = 0.3811 target = 0.079272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.062254 restraints weight = 85650.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.063587 restraints weight = 60121.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064216 restraints weight = 46151.581| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13182 Z= 0.165 Angle : 0.584 7.731 17946 Z= 0.313 Chirality : 0.042 0.373 2226 Planarity : 0.005 0.055 2320 Dihedral : 3.745 17.138 1945 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.19), residues: 1830 helix: 1.62 (0.13), residues: 1486 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 344 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 0.036 0.002 PHE I 62 TYR 0.014 0.001 TYR H 48 ARG 0.007 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1284) hydrogen bonds : angle 3.84078 ( 3831) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.39957 ( 4) covalent geometry : bond 0.00348 (13180) covalent geometry : angle 0.58450 (17942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9091 (mmp) cc_final: 0.8616 (mmm) REVERT: Y 115 GLN cc_start: 0.9242 (pt0) cc_final: 0.8898 (pm20) REVERT: Y 119 ARG cc_start: 0.9635 (mtt180) cc_final: 0.9417 (ptp-110) REVERT: V 34 MET cc_start: 0.8936 (tpt) cc_final: 0.8717 (tmm) REVERT: H 50 PHE cc_start: 0.8859 (m-80) cc_final: 0.8606 (m-10) REVERT: H 53 ILE cc_start: 0.9000 (tp) cc_final: 0.8553 (tp) REVERT: H 55 PHE cc_start: 0.8991 (m-80) cc_final: 0.8536 (m-80) REVERT: H 57 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8523 (pt0) REVERT: I 48 TYR cc_start: 0.9026 (m-80) cc_final: 0.8170 (m-80) REVERT: I 49 MET cc_start: 0.9211 (ttp) cc_final: 0.8767 (tmm) REVERT: I 57 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8016 (mt-10) REVERT: K 20 PRO cc_start: 0.9451 (Cg_exo) cc_final: 0.9233 (Cg_endo) REVERT: K 53 ILE cc_start: 0.9473 (mm) cc_final: 0.8878 (tp) REVERT: K 57 GLU cc_start: 0.9337 (tp30) cc_final: 0.8751 (pt0) REVERT: L 1 MET cc_start: 0.7621 (tpt) cc_final: 0.7388 (tmm) REVERT: L 24 ILE cc_start: 0.9391 (mt) cc_final: 0.9054 (mm) REVERT: L 26 ILE cc_start: 0.9783 (mt) cc_final: 0.9470 (tt) REVERT: L 29 SER cc_start: 0.9630 (t) cc_final: 0.9325 (p) REVERT: L 33 GLN cc_start: 0.9436 (tt0) cc_final: 0.9071 (mm110) REVERT: L 48 TYR cc_start: 0.8855 (m-80) cc_final: 0.7768 (m-80) REVERT: L 57 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8142 (pt0) REVERT: L 62 PHE cc_start: 0.8761 (m-10) cc_final: 0.8462 (m-80) REVERT: M 41 ILE cc_start: 0.8819 (tp) cc_final: 0.8354 (tt) REVERT: N 43 ASN cc_start: 0.8977 (p0) cc_final: 0.8686 (p0) REVERT: N 51 ILE cc_start: 0.9440 (mt) cc_final: 0.9067 (tt) REVERT: N 55 PHE cc_start: 0.9413 (m-10) cc_final: 0.9182 (m-80) REVERT: N 57 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8113 (pt0) REVERT: N 66 ILE cc_start: 0.9352 (mm) cc_final: 0.9110 (mm) REVERT: O 50 PHE cc_start: 0.9142 (m-10) cc_final: 0.8797 (m-80) REVERT: O 57 GLU cc_start: 0.9467 (tp30) cc_final: 0.8888 (tp30) REVERT: O 59 LEU cc_start: 0.9590 (mt) cc_final: 0.9326 (mp) REVERT: P 27 ILE cc_start: 0.9092 (mt) cc_final: 0.8872 (mt) REVERT: P 33 GLN cc_start: 0.9593 (mt0) cc_final: 0.9168 (mm-40) REVERT: P 53 ILE cc_start: 0.9513 (pt) cc_final: 0.9226 (pt) REVERT: P 56 THR cc_start: 0.9234 (p) cc_final: 0.9006 (p) REVERT: P 57 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9224 (mm-30) REVERT: Q 1 MET cc_start: 0.6518 (mmm) cc_final: 0.5886 (mmm) REVERT: Q 50 PHE cc_start: 0.9404 (m-80) cc_final: 0.9064 (m-80) REVERT: Q 55 PHE cc_start: 0.9266 (m-10) cc_final: 0.9003 (m-80) REVERT: Q 68 PHE cc_start: 0.9018 (m-80) cc_final: 0.8675 (m-80) REVERT: T 244 PHE cc_start: 0.9097 (m-80) cc_final: 0.8797 (m-80) REVERT: T 264 MET cc_start: 0.9047 (mmt) cc_final: 0.8722 (tpp) REVERT: Z 125 LEU cc_start: 0.9159 (mp) cc_final: 0.7665 (mp) REVERT: Z 206 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8948 (mm-30) REVERT: Z 280 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8659 (tm-30) REVERT: Z 281 VAL cc_start: 0.9426 (p) cc_final: 0.8848 (p) outliers start: 2 outliers final: 2 residues processed: 382 average time/residue: 0.1903 time to fit residues: 111.2379 Evaluate side-chains 322 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 40.0000 chunk 163 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 92 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 115 GLN V 149 HIS J 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.080016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.062929 restraints weight = 87908.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064231 restraints weight = 60727.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.065150 restraints weight = 47000.145| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13182 Z= 0.145 Angle : 0.588 8.660 17946 Z= 0.310 Chirality : 0.042 0.411 2226 Planarity : 0.004 0.056 2320 Dihedral : 3.747 16.416 1945 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.09 % Allowed : 2.46 % Favored : 97.45 % 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: 1.55 (0.19), residues: 1830 helix: 1.60 (0.13), residues: 1487 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.031 0.001 PHE O 62 TYR 0.013 0.001 TYR H 48 ARG 0.004 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 1284) hydrogen bonds : angle 3.78725 ( 3831) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.47255 ( 4) covalent geometry : bond 0.00310 (13180) covalent geometry : angle 0.58850 (17942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9096 (mmp) cc_final: 0.8678 (mmm) REVERT: Y 90 GLN cc_start: 0.9062 (mp10) cc_final: 0.8727 (mp10) REVERT: Y 132 VAL cc_start: 0.9477 (p) cc_final: 0.9224 (m) REVERT: V 34 MET cc_start: 0.8978 (tpt) cc_final: 0.8748 (tmm) REVERT: H 50 PHE cc_start: 0.8846 (m-80) cc_final: 0.8578 (m-10) REVERT: H 51 ILE cc_start: 0.9403 (mt) cc_final: 0.9044 (mt) REVERT: H 53 ILE cc_start: 0.8975 (tp) cc_final: 0.8542 (tp) REVERT: H 55 PHE cc_start: 0.8753 (m-80) cc_final: 0.8464 (m-80) REVERT: H 57 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8425 (pt0) REVERT: I 29 SER cc_start: 0.9316 (t) cc_final: 0.9076 (p) REVERT: I 48 TYR cc_start: 0.9036 (m-80) cc_final: 0.8163 (m-80) REVERT: I 49 MET cc_start: 0.9157 (ttp) cc_final: 0.8820 (tmm) REVERT: I 53 ILE cc_start: 0.8988 (tt) cc_final: 0.8695 (tt) REVERT: I 57 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8014 (mt-10) REVERT: K 20 PRO cc_start: 0.9470 (Cg_exo) cc_final: 0.9258 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9426 (m-80) cc_final: 0.8747 (m-80) REVERT: K 53 ILE cc_start: 0.9544 (mm) cc_final: 0.8765 (tp) REVERT: K 57 GLU cc_start: 0.9316 (tp30) cc_final: 0.8716 (pt0) REVERT: L 24 ILE cc_start: 0.9387 (mt) cc_final: 0.9011 (mm) REVERT: L 26 ILE cc_start: 0.9782 (mt) cc_final: 0.9471 (tt) REVERT: L 29 SER cc_start: 0.9607 (t) cc_final: 0.9310 (p) REVERT: L 33 GLN cc_start: 0.9418 (tt0) cc_final: 0.9078 (mm110) REVERT: L 41 ILE cc_start: 0.8941 (tp) cc_final: 0.8731 (tp) REVERT: L 48 TYR cc_start: 0.8771 (m-80) cc_final: 0.7754 (m-80) REVERT: L 57 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8233 (pt0) REVERT: L 62 PHE cc_start: 0.8710 (m-10) cc_final: 0.8449 (m-80) REVERT: M 41 ILE cc_start: 0.8776 (tp) cc_final: 0.8333 (tt) REVERT: M 66 ILE cc_start: 0.8972 (mm) cc_final: 0.8561 (mm) REVERT: N 43 ASN cc_start: 0.9005 (p0) cc_final: 0.8713 (p0) REVERT: N 51 ILE cc_start: 0.9430 (mt) cc_final: 0.9024 (tt) REVERT: N 55 PHE cc_start: 0.9297 (m-10) cc_final: 0.9051 (m-80) REVERT: N 57 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8128 (mt-10) REVERT: N 62 PHE cc_start: 0.9304 (m-10) cc_final: 0.9051 (m-80) REVERT: N 66 ILE cc_start: 0.9322 (mm) cc_final: 0.9081 (mm) REVERT: O 50 PHE cc_start: 0.9136 (m-10) cc_final: 0.8786 (m-80) REVERT: O 57 GLU cc_start: 0.9468 (tp30) cc_final: 0.8865 (tp30) REVERT: O 62 PHE cc_start: 0.9124 (m-80) cc_final: 0.8838 (m-80) REVERT: P 27 ILE cc_start: 0.9108 (mt) cc_final: 0.8903 (mt) REVERT: P 53 ILE cc_start: 0.9510 (pt) cc_final: 0.9275 (pt) REVERT: P 57 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9231 (mm-30) REVERT: P 62 PHE cc_start: 0.9243 (m-80) cc_final: 0.8931 (m-80) REVERT: P 64 LEU cc_start: 0.9691 (mt) cc_final: 0.9432 (mt) REVERT: P 68 PHE cc_start: 0.9076 (m-80) cc_final: 0.8432 (m-80) REVERT: Q 1 MET cc_start: 0.6354 (mmm) cc_final: 0.5744 (mmm) REVERT: Q 50 PHE cc_start: 0.9404 (m-80) cc_final: 0.9092 (m-80) REVERT: Q 55 PHE cc_start: 0.9232 (m-10) cc_final: 0.8933 (m-80) REVERT: Q 57 GLU cc_start: 0.9163 (pm20) cc_final: 0.8555 (pm20) REVERT: Q 68 PHE cc_start: 0.8996 (m-80) cc_final: 0.8678 (m-80) REVERT: T 244 PHE cc_start: 0.9098 (m-80) cc_final: 0.8809 (m-80) REVERT: T 264 MET cc_start: 0.9028 (mmt) cc_final: 0.8712 (tpp) REVERT: Z 206 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8958 (mm-30) REVERT: Z 280 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8638 (tp30) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.2000 time to fit residues: 117.9558 Evaluate side-chains 319 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 149 HIS ** T 287 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.077140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.060215 restraints weight = 90262.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061444 restraints weight = 63101.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.062233 restraints weight = 48738.025| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13182 Z= 0.226 Angle : 0.655 8.453 17946 Z= 0.356 Chirality : 0.044 0.369 2226 Planarity : 0.005 0.059 2320 Dihedral : 3.887 18.267 1945 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.18 % Allowed : 1.46 % Favored : 98.36 % 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: 1830 helix: 1.39 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.52 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 208 HIS 0.007 0.001 HIS V 149 PHE 0.037 0.002 PHE I 62 TYR 0.015 0.002 TYR H 48 ARG 0.005 0.001 ARG Q 44 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 1284) hydrogen bonds : angle 4.05156 ( 3831) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.47429 ( 4) covalent geometry : bond 0.00467 (13180) covalent geometry : angle 0.65468 (17942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9162 (mmp) cc_final: 0.8756 (mmm) REVERT: H 50 PHE cc_start: 0.8835 (m-80) cc_final: 0.8611 (m-10) REVERT: H 51 ILE cc_start: 0.9444 (mt) cc_final: 0.9139 (mt) REVERT: H 55 PHE cc_start: 0.8826 (m-80) cc_final: 0.8603 (m-80) REVERT: H 57 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8456 (pt0) REVERT: I 1 MET cc_start: 0.8033 (mtp) cc_final: 0.7786 (mtp) REVERT: I 48 TYR cc_start: 0.9097 (m-80) cc_final: 0.8246 (m-80) REVERT: I 49 MET cc_start: 0.9249 (ttp) cc_final: 0.8764 (tmm) REVERT: I 53 ILE cc_start: 0.9124 (tt) cc_final: 0.8715 (tt) REVERT: I 57 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8114 (mt-10) REVERT: J 55 PHE cc_start: 0.9232 (m-80) cc_final: 0.9011 (m-80) REVERT: K 20 PRO cc_start: 0.9486 (Cg_exo) cc_final: 0.9267 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9457 (m-80) cc_final: 0.8751 (m-80) REVERT: K 53 ILE cc_start: 0.9591 (mm) cc_final: 0.8971 (tp) REVERT: K 57 GLU cc_start: 0.9314 (tp30) cc_final: 0.8858 (mt-10) REVERT: L 24 ILE cc_start: 0.9406 (mt) cc_final: 0.9172 (mm) REVERT: L 26 ILE cc_start: 0.9781 (mt) cc_final: 0.9525 (tt) REVERT: L 29 SER cc_start: 0.9632 (t) cc_final: 0.9312 (p) REVERT: L 33 GLN cc_start: 0.9454 (tt0) cc_final: 0.9127 (mm110) REVERT: L 48 TYR cc_start: 0.8865 (m-80) cc_final: 0.8036 (m-80) REVERT: L 62 PHE cc_start: 0.8711 (m-10) cc_final: 0.8488 (m-80) REVERT: M 1 MET cc_start: 0.7271 (mmp) cc_final: 0.6796 (mmm) REVERT: M 41 ILE cc_start: 0.8943 (tp) cc_final: 0.8521 (tt) REVERT: N 1 MET cc_start: 0.6501 (mtp) cc_final: 0.5979 (mtp) REVERT: N 43 ASN cc_start: 0.8982 (p0) cc_final: 0.8697 (p0) REVERT: N 51 ILE cc_start: 0.9439 (mt) cc_final: 0.9119 (mt) REVERT: N 62 PHE cc_start: 0.9323 (m-10) cc_final: 0.9079 (m-80) REVERT: N 66 ILE cc_start: 0.9412 (mm) cc_final: 0.9178 (mm) REVERT: O 50 PHE cc_start: 0.9255 (m-10) cc_final: 0.8749 (m-80) REVERT: O 57 GLU cc_start: 0.9476 (tp30) cc_final: 0.8869 (tp30) REVERT: O 62 PHE cc_start: 0.9179 (m-80) cc_final: 0.8884 (m-80) REVERT: P 27 ILE cc_start: 0.9157 (mt) cc_final: 0.8956 (mt) REVERT: P 59 LEU cc_start: 0.9495 (mm) cc_final: 0.9232 (mm) REVERT: P 62 PHE cc_start: 0.9257 (m-80) cc_final: 0.8895 (m-80) REVERT: P 68 PHE cc_start: 0.9228 (m-80) cc_final: 0.8845 (m-80) REVERT: Q 1 MET cc_start: 0.6476 (mmm) cc_final: 0.5890 (mmm) REVERT: Q 55 PHE cc_start: 0.9254 (m-10) cc_final: 0.8839 (m-80) REVERT: Q 68 PHE cc_start: 0.9087 (m-80) cc_final: 0.8685 (m-80) REVERT: T 264 MET cc_start: 0.9031 (mmt) cc_final: 0.8758 (tpp) REVERT: Z 84 MET cc_start: 0.9226 (tpp) cc_final: 0.8865 (tpp) REVERT: Z 125 LEU cc_start: 0.9226 (mp) cc_final: 0.8943 (mm) REVERT: Z 206 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9054 (mm-30) REVERT: Z 235 GLU cc_start: 0.8428 (pt0) cc_final: 0.8213 (pt0) REVERT: Z 280 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8724 (tm-30) outliers start: 2 outliers final: 1 residues processed: 359 average time/residue: 0.2003 time to fit residues: 109.4188 Evaluate side-chains 292 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 95 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.078601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061507 restraints weight = 87311.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062780 restraints weight = 61493.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.063587 restraints weight = 47682.454| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13182 Z= 0.157 Angle : 0.629 12.549 17946 Z= 0.333 Chirality : 0.043 0.315 2226 Planarity : 0.005 0.062 2320 Dihedral : 3.840 18.072 1945 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 1.39 (0.19), residues: 1830 helix: 1.48 (0.13), residues: 1485 sheet: None (None), residues: 0 loop : -1.47 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 136 PHE 0.034 0.002 PHE Q 62 TYR 0.015 0.001 TYR H 48 ARG 0.007 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 1284) hydrogen bonds : angle 3.93178 ( 3831) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.44826 ( 4) covalent geometry : bond 0.00341 (13180) covalent geometry : angle 0.62875 (17942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9143 (mmp) cc_final: 0.8754 (mmm) REVERT: Y 90 GLN cc_start: 0.9075 (mp10) cc_final: 0.8788 (mp10) REVERT: Y 115 GLN cc_start: 0.8621 (pp30) cc_final: 0.8211 (pp30) REVERT: V 25 LEU cc_start: 0.9636 (mt) cc_final: 0.9431 (mt) REVERT: V 82 GLN cc_start: 0.9388 (tp-100) cc_final: 0.9080 (tp-100) REVERT: V 84 GLN cc_start: 0.9149 (pt0) cc_final: 0.8799 (pm20) REVERT: X 18 PHE cc_start: 0.3490 (t80) cc_final: 0.3231 (m-80) REVERT: X 21 LEU cc_start: 0.7857 (pp) cc_final: 0.7635 (pp) REVERT: H 50 PHE cc_start: 0.8835 (m-80) cc_final: 0.8615 (m-10) REVERT: H 51 ILE cc_start: 0.9436 (mt) cc_final: 0.9090 (mt) REVERT: H 53 ILE cc_start: 0.9080 (tp) cc_final: 0.8680 (tp) REVERT: H 55 PHE cc_start: 0.8776 (m-80) cc_final: 0.8505 (m-80) REVERT: H 57 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8466 (pt0) REVERT: I 1 MET cc_start: 0.8203 (mtp) cc_final: 0.8002 (mtp) REVERT: I 29 SER cc_start: 0.9314 (t) cc_final: 0.9058 (p) REVERT: I 48 TYR cc_start: 0.9026 (m-80) cc_final: 0.8153 (m-80) REVERT: I 49 MET cc_start: 0.9192 (ttp) cc_final: 0.8788 (tmm) REVERT: I 53 ILE cc_start: 0.9101 (tt) cc_final: 0.8687 (tt) REVERT: I 57 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7999 (mt-10) REVERT: J 55 PHE cc_start: 0.9149 (m-80) cc_final: 0.8900 (m-80) REVERT: K 48 TYR cc_start: 0.9443 (m-80) cc_final: 0.8991 (m-80) REVERT: K 53 ILE cc_start: 0.9390 (mm) cc_final: 0.8897 (tp) REVERT: K 57 GLU cc_start: 0.9308 (tp30) cc_final: 0.8729 (pt0) REVERT: L 15 LEU cc_start: 0.9065 (mp) cc_final: 0.8813 (mp) REVERT: L 26 ILE cc_start: 0.9775 (mt) cc_final: 0.9492 (tt) REVERT: L 29 SER cc_start: 0.9609 (t) cc_final: 0.9278 (p) REVERT: L 33 GLN cc_start: 0.9451 (tt0) cc_final: 0.9084 (mm110) REVERT: L 41 ILE cc_start: 0.8963 (tp) cc_final: 0.8763 (tp) REVERT: L 48 TYR cc_start: 0.8834 (m-80) cc_final: 0.8000 (m-80) REVERT: L 62 PHE cc_start: 0.8684 (m-10) cc_final: 0.8450 (m-80) REVERT: M 1 MET cc_start: 0.7223 (mmp) cc_final: 0.6916 (mmm) REVERT: M 4 LEU cc_start: 0.9389 (tp) cc_final: 0.9164 (tp) REVERT: M 41 ILE cc_start: 0.8941 (tp) cc_final: 0.8486 (tt) REVERT: N 1 MET cc_start: 0.6536 (mtp) cc_final: 0.6256 (mtp) REVERT: N 43 ASN cc_start: 0.8994 (p0) cc_final: 0.8728 (p0) REVERT: N 51 ILE cc_start: 0.9394 (mt) cc_final: 0.9144 (mt) REVERT: N 55 PHE cc_start: 0.9106 (m-80) cc_final: 0.8730 (m-80) REVERT: N 62 PHE cc_start: 0.9326 (m-10) cc_final: 0.9097 (m-80) REVERT: N 66 ILE cc_start: 0.9349 (mm) cc_final: 0.9113 (mm) REVERT: O 40 GLU cc_start: 0.9331 (mp0) cc_final: 0.9099 (pp20) REVERT: O 50 PHE cc_start: 0.9230 (m-10) cc_final: 0.8776 (m-80) REVERT: O 57 GLU cc_start: 0.9498 (tp30) cc_final: 0.8894 (tp30) REVERT: P 27 ILE cc_start: 0.9144 (mt) cc_final: 0.8929 (mt) REVERT: P 59 LEU cc_start: 0.9488 (mm) cc_final: 0.9227 (mm) REVERT: P 62 PHE cc_start: 0.9219 (m-80) cc_final: 0.8875 (m-80) REVERT: P 68 PHE cc_start: 0.9202 (m-80) cc_final: 0.8770 (m-80) REVERT: Q 1 MET cc_start: 0.6398 (mmm) cc_final: 0.5813 (mmm) REVERT: Q 53 ILE cc_start: 0.8531 (mt) cc_final: 0.8270 (mt) REVERT: Q 55 PHE cc_start: 0.9189 (m-10) cc_final: 0.8892 (m-80) REVERT: Q 57 GLU cc_start: 0.9059 (pm20) cc_final: 0.8775 (pm20) REVERT: Q 68 PHE cc_start: 0.9018 (m-80) cc_final: 0.8648 (m-80) REVERT: T 244 PHE cc_start: 0.9077 (m-80) cc_final: 0.8786 (m-80) REVERT: T 264 MET cc_start: 0.9052 (mmt) cc_final: 0.8810 (tpp) REVERT: Z 84 MET cc_start: 0.9303 (tpp) cc_final: 0.8962 (tpp) REVERT: Z 125 LEU cc_start: 0.9343 (mp) cc_final: 0.9104 (mm) REVERT: Z 206 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9028 (mm-30) REVERT: Z 235 GLU cc_start: 0.8448 (pt0) cc_final: 0.8234 (pt0) REVERT: Z 264 MET cc_start: 0.9307 (mmm) cc_final: 0.9038 (mmm) REVERT: Z 280 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8737 (tm-30) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1995 time to fit residues: 112.0135 Evaluate side-chains 314 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 121 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.078458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.061749 restraints weight = 90693.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062996 restraints weight = 63259.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063744 restraints weight = 48741.846| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13182 Z= 0.175 Angle : 0.650 9.731 17946 Z= 0.351 Chirality : 0.044 0.424 2226 Planarity : 0.005 0.066 2320 Dihedral : 3.849 16.909 1945 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 1.43 (0.19), residues: 1830 helix: 1.51 (0.13), residues: 1494 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 136 PHE 0.037 0.002 PHE I 62 TYR 0.016 0.001 TYR H 48 ARG 0.005 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1284) hydrogen bonds : angle 3.94487 ( 3831) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.41597 ( 4) covalent geometry : bond 0.00388 (13180) covalent geometry : angle 0.64992 (17942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9164 (mmp) cc_final: 0.8788 (mmm) REVERT: Y 90 GLN cc_start: 0.9093 (mp10) cc_final: 0.8806 (mp10) REVERT: V 82 GLN cc_start: 0.9427 (tp-100) cc_final: 0.9139 (tp-100) REVERT: V 84 GLN cc_start: 0.9127 (pt0) cc_final: 0.8900 (pt0) REVERT: X 18 PHE cc_start: 0.3504 (t80) cc_final: 0.3200 (m-80) REVERT: X 21 LEU cc_start: 0.7842 (pp) cc_final: 0.7611 (pp) REVERT: H 49 MET cc_start: 0.9132 (ppp) cc_final: 0.8583 (ppp) REVERT: H 50 PHE cc_start: 0.8787 (m-80) cc_final: 0.8457 (m-10) REVERT: H 51 ILE cc_start: 0.9458 (mt) cc_final: 0.9165 (mt) REVERT: H 53 ILE cc_start: 0.9030 (tp) cc_final: 0.8654 (tp) REVERT: H 55 PHE cc_start: 0.8753 (m-80) cc_final: 0.8496 (m-80) REVERT: H 57 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8456 (pt0) REVERT: H 62 PHE cc_start: 0.9056 (m-10) cc_final: 0.8827 (m-80) REVERT: I 1 MET cc_start: 0.8432 (mtp) cc_final: 0.7860 (ttt) REVERT: I 48 TYR cc_start: 0.9065 (m-80) cc_final: 0.8216 (m-80) REVERT: I 49 MET cc_start: 0.9207 (ttp) cc_final: 0.8781 (tmm) REVERT: I 53 ILE cc_start: 0.9141 (tt) cc_final: 0.8733 (tt) REVERT: I 57 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8058 (mt-10) REVERT: J 20 PRO cc_start: 0.9161 (Cg_exo) cc_final: 0.8958 (Cg_endo) REVERT: J 55 PHE cc_start: 0.9173 (m-80) cc_final: 0.8912 (m-80) REVERT: K 48 TYR cc_start: 0.9445 (m-80) cc_final: 0.8976 (m-80) REVERT: K 53 ILE cc_start: 0.9604 (mm) cc_final: 0.8830 (tp) REVERT: K 57 GLU cc_start: 0.9310 (tp30) cc_final: 0.8698 (pt0) REVERT: L 15 LEU cc_start: 0.9086 (mp) cc_final: 0.8827 (mp) REVERT: L 26 ILE cc_start: 0.9769 (mt) cc_final: 0.9460 (tt) REVERT: L 29 SER cc_start: 0.9592 (t) cc_final: 0.9263 (p) REVERT: L 33 GLN cc_start: 0.9466 (tt0) cc_final: 0.9070 (mm110) REVERT: L 62 PHE cc_start: 0.8735 (m-10) cc_final: 0.8513 (m-80) REVERT: M 1 MET cc_start: 0.7237 (mmp) cc_final: 0.6860 (mmm) REVERT: M 4 LEU cc_start: 0.9418 (tp) cc_final: 0.9200 (tp) REVERT: M 41 ILE cc_start: 0.8923 (tp) cc_final: 0.8466 (tt) REVERT: N 1 MET cc_start: 0.6569 (mtp) cc_final: 0.6304 (mtp) REVERT: N 43 ASN cc_start: 0.9004 (p0) cc_final: 0.8741 (p0) REVERT: N 51 ILE cc_start: 0.9373 (mt) cc_final: 0.9040 (mt) REVERT: N 55 PHE cc_start: 0.9112 (m-80) cc_final: 0.8650 (m-80) REVERT: N 62 PHE cc_start: 0.9336 (m-10) cc_final: 0.9101 (m-80) REVERT: N 66 ILE cc_start: 0.9349 (mm) cc_final: 0.9117 (mm) REVERT: O 40 GLU cc_start: 0.9370 (mp0) cc_final: 0.9158 (pp20) REVERT: O 50 PHE cc_start: 0.9253 (m-10) cc_final: 0.8806 (m-80) REVERT: O 57 GLU cc_start: 0.9617 (tp30) cc_final: 0.8944 (tp30) REVERT: P 27 ILE cc_start: 0.9167 (mt) cc_final: 0.8948 (mt) REVERT: P 59 LEU cc_start: 0.9487 (mm) cc_final: 0.9231 (mm) REVERT: P 62 PHE cc_start: 0.9216 (m-80) cc_final: 0.8881 (m-80) REVERT: P 68 PHE cc_start: 0.9259 (m-80) cc_final: 0.8793 (m-80) REVERT: Q 1 MET cc_start: 0.6355 (mmm) cc_final: 0.5764 (mmm) REVERT: Q 55 PHE cc_start: 0.9192 (m-10) cc_final: 0.8885 (m-80) REVERT: Q 68 PHE cc_start: 0.9086 (m-80) cc_final: 0.8664 (m-80) REVERT: T 244 PHE cc_start: 0.9085 (m-80) cc_final: 0.8828 (m-80) REVERT: T 264 MET cc_start: 0.9048 (mmt) cc_final: 0.8794 (tpp) REVERT: Z 84 MET cc_start: 0.9290 (tpp) cc_final: 0.9024 (tpp) REVERT: Z 125 LEU cc_start: 0.9309 (mp) cc_final: 0.9014 (mp) REVERT: Z 206 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9062 (mm-30) REVERT: Z 264 MET cc_start: 0.9391 (mmm) cc_final: 0.9088 (mmm) REVERT: Z 280 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8940 (tm-30) REVERT: Z 286 ILE cc_start: 0.9779 (tp) cc_final: 0.9542 (tp) REVERT: Z 290 ILE cc_start: 0.9629 (mm) cc_final: 0.9384 (mm) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2071 time to fit residues: 115.5668 Evaluate side-chains 299 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 40.0000 chunk 177 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.078551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.061695 restraints weight = 88499.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.062939 restraints weight = 61980.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063797 restraints weight = 48051.645| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13182 Z= 0.165 Angle : 0.661 10.739 17946 Z= 0.353 Chirality : 0.045 0.355 2226 Planarity : 0.005 0.069 2320 Dihedral : 3.863 17.256 1945 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 1.48 (0.19), residues: 1830 helix: 1.51 (0.13), residues: 1505 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 136 PHE 0.032 0.002 PHE Q 62 TYR 0.019 0.002 TYR H 48 ARG 0.006 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 1284) hydrogen bonds : angle 3.96947 ( 3831) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.40091 ( 4) covalent geometry : bond 0.00363 (13180) covalent geometry : angle 0.66132 (17942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9092 (mmp) cc_final: 0.8751 (mmm) REVERT: V 84 GLN cc_start: 0.9090 (pt0) cc_final: 0.8717 (pt0) REVERT: H 29 SER cc_start: 0.9398 (t) cc_final: 0.9146 (m) REVERT: H 50 PHE cc_start: 0.8776 (m-80) cc_final: 0.8526 (m-10) REVERT: H 51 ILE cc_start: 0.9441 (mt) cc_final: 0.9154 (mt) REVERT: H 53 ILE cc_start: 0.9047 (tp) cc_final: 0.8629 (tp) REVERT: H 55 PHE cc_start: 0.8769 (m-80) cc_final: 0.8396 (m-80) REVERT: H 57 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8461 (pt0) REVERT: H 62 PHE cc_start: 0.9050 (m-10) cc_final: 0.8815 (m-80) REVERT: I 1 MET cc_start: 0.8363 (mtp) cc_final: 0.7811 (ttt) REVERT: I 29 SER cc_start: 0.9352 (t) cc_final: 0.9092 (p) REVERT: I 48 TYR cc_start: 0.9027 (m-80) cc_final: 0.8167 (m-80) REVERT: I 49 MET cc_start: 0.9218 (ttp) cc_final: 0.8783 (tmm) REVERT: I 57 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7664 (mp0) REVERT: J 20 PRO cc_start: 0.9043 (Cg_exo) cc_final: 0.8815 (Cg_endo) REVERT: J 55 PHE cc_start: 0.9125 (m-80) cc_final: 0.8903 (m-80) REVERT: K 48 TYR cc_start: 0.9396 (m-80) cc_final: 0.8957 (m-80) REVERT: K 53 ILE cc_start: 0.9625 (mm) cc_final: 0.9198 (mm) REVERT: K 57 GLU cc_start: 0.9256 (tp30) cc_final: 0.8671 (pt0) REVERT: L 26 ILE cc_start: 0.9779 (mt) cc_final: 0.9486 (tt) REVERT: L 29 SER cc_start: 0.9592 (t) cc_final: 0.9334 (p) REVERT: L 33 GLN cc_start: 0.9456 (tt0) cc_final: 0.9104 (tp40) REVERT: L 48 TYR cc_start: 0.9168 (m-80) cc_final: 0.8207 (m-80) REVERT: L 56 THR cc_start: 0.9311 (t) cc_final: 0.9080 (t) REVERT: L 62 PHE cc_start: 0.8626 (m-10) cc_final: 0.8417 (m-80) REVERT: M 1 MET cc_start: 0.7162 (mmp) cc_final: 0.6806 (mmm) REVERT: M 4 LEU cc_start: 0.9384 (tp) cc_final: 0.9154 (tp) REVERT: M 41 ILE cc_start: 0.8934 (tp) cc_final: 0.8353 (tt) REVERT: N 1 MET cc_start: 0.6441 (mtp) cc_final: 0.6223 (mtp) REVERT: N 43 ASN cc_start: 0.8976 (p0) cc_final: 0.8707 (p0) REVERT: N 51 ILE cc_start: 0.9356 (mt) cc_final: 0.9027 (mt) REVERT: N 55 PHE cc_start: 0.9037 (m-80) cc_final: 0.8608 (m-80) REVERT: N 62 PHE cc_start: 0.9290 (m-10) cc_final: 0.9048 (m-80) REVERT: N 66 ILE cc_start: 0.9359 (mm) cc_final: 0.9132 (mm) REVERT: O 50 PHE cc_start: 0.9239 (m-10) cc_final: 0.8781 (m-80) REVERT: O 57 GLU cc_start: 0.9559 (tp30) cc_final: 0.8820 (tp30) REVERT: P 27 ILE cc_start: 0.9182 (mt) cc_final: 0.8977 (mt) REVERT: P 59 LEU cc_start: 0.9498 (mm) cc_final: 0.9240 (mm) REVERT: P 62 PHE cc_start: 0.9159 (m-80) cc_final: 0.8862 (m-80) REVERT: P 68 PHE cc_start: 0.9196 (m-80) cc_final: 0.8730 (m-80) REVERT: Q 1 MET cc_start: 0.6234 (mmm) cc_final: 0.5836 (mmp) REVERT: Q 50 PHE cc_start: 0.9407 (m-80) cc_final: 0.9134 (m-80) REVERT: Q 55 PHE cc_start: 0.9183 (m-10) cc_final: 0.8861 (m-80) REVERT: Q 68 PHE cc_start: 0.9031 (m-80) cc_final: 0.8667 (m-80) REVERT: T 244 PHE cc_start: 0.9041 (m-80) cc_final: 0.8771 (m-80) REVERT: T 264 MET cc_start: 0.9049 (mmt) cc_final: 0.8813 (tpp) REVERT: T 282 PHE cc_start: 0.8986 (t80) cc_final: 0.8686 (t80) REVERT: T 286 ILE cc_start: 0.9435 (pt) cc_final: 0.9202 (pt) REVERT: Z 84 MET cc_start: 0.9204 (tpp) cc_final: 0.8840 (tpp) REVERT: Z 206 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9031 (mm-30) REVERT: Z 280 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8597 (tm-30) REVERT: Z 286 ILE cc_start: 0.9749 (tp) cc_final: 0.9520 (tp) REVERT: Z 290 ILE cc_start: 0.9615 (mm) cc_final: 0.9383 (mm) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2033 time to fit residues: 112.8720 Evaluate side-chains 302 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.077718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.061201 restraints weight = 89238.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.062355 restraints weight = 63038.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063024 restraints weight = 49014.530| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13182 Z= 0.188 Angle : 0.671 10.417 17946 Z= 0.360 Chirality : 0.044 0.312 2226 Planarity : 0.005 0.067 2320 Dihedral : 3.881 17.136 1945 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 1.49 (0.19), residues: 1830 helix: 1.53 (0.13), residues: 1493 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 136 PHE 0.033 0.002 PHE I 62 TYR 0.028 0.002 TYR Z 277 ARG 0.006 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 1284) hydrogen bonds : angle 4.03943 ( 3831) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.33440 ( 4) covalent geometry : bond 0.00416 (13180) covalent geometry : angle 0.67119 (17942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9201 (mmp) cc_final: 0.8824 (mmm) REVERT: V 34 MET cc_start: 0.9165 (mmm) cc_final: 0.8749 (mmp) REVERT: H 29 SER cc_start: 0.9361 (t) cc_final: 0.9105 (m) REVERT: H 49 MET cc_start: 0.9104 (ppp) cc_final: 0.8595 (ppp) REVERT: H 50 PHE cc_start: 0.8776 (m-80) cc_final: 0.8452 (m-10) REVERT: H 51 ILE cc_start: 0.9477 (mt) cc_final: 0.9171 (mt) REVERT: H 53 ILE cc_start: 0.8991 (tp) cc_final: 0.8650 (tp) REVERT: H 57 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8399 (pt0) REVERT: H 62 PHE cc_start: 0.9118 (m-10) cc_final: 0.8863 (m-80) REVERT: I 1 MET cc_start: 0.8388 (mtp) cc_final: 0.7803 (ttt) REVERT: I 29 SER cc_start: 0.9329 (t) cc_final: 0.9067 (p) REVERT: I 48 TYR cc_start: 0.9091 (m-80) cc_final: 0.8213 (m-80) REVERT: I 49 MET cc_start: 0.9189 (ttp) cc_final: 0.8773 (tmm) REVERT: J 20 PRO cc_start: 0.9041 (Cg_exo) cc_final: 0.8837 (Cg_endo) REVERT: J 55 PHE cc_start: 0.9167 (m-80) cc_final: 0.8945 (m-80) REVERT: K 48 TYR cc_start: 0.9417 (m-80) cc_final: 0.8947 (m-80) REVERT: K 53 ILE cc_start: 0.9620 (mm) cc_final: 0.9207 (mm) REVERT: K 57 GLU cc_start: 0.9286 (tp30) cc_final: 0.8697 (pt0) REVERT: L 26 ILE cc_start: 0.9768 (mt) cc_final: 0.9459 (tt) REVERT: L 29 SER cc_start: 0.9579 (t) cc_final: 0.9297 (p) REVERT: L 33 GLN cc_start: 0.9470 (tt0) cc_final: 0.9079 (tp40) REVERT: L 48 TYR cc_start: 0.9214 (m-80) cc_final: 0.8305 (m-80) REVERT: L 62 PHE cc_start: 0.8724 (m-10) cc_final: 0.8494 (m-80) REVERT: M 1 MET cc_start: 0.7273 (mmp) cc_final: 0.6844 (mmm) REVERT: M 4 LEU cc_start: 0.9401 (tp) cc_final: 0.9167 (tp) REVERT: M 41 ILE cc_start: 0.8959 (tp) cc_final: 0.8523 (tt) REVERT: N 1 MET cc_start: 0.6491 (mtp) cc_final: 0.6282 (mtp) REVERT: N 27 ILE cc_start: 0.9367 (mt) cc_final: 0.9139 (pt) REVERT: N 43 ASN cc_start: 0.9005 (p0) cc_final: 0.8744 (p0) REVERT: N 51 ILE cc_start: 0.9370 (mt) cc_final: 0.9043 (mt) REVERT: N 55 PHE cc_start: 0.9098 (m-80) cc_final: 0.8672 (m-80) REVERT: N 62 PHE cc_start: 0.9331 (m-10) cc_final: 0.9104 (m-80) REVERT: N 66 ILE cc_start: 0.9359 (mm) cc_final: 0.9122 (mm) REVERT: O 50 PHE cc_start: 0.9147 (m-10) cc_final: 0.8873 (m-80) REVERT: O 57 GLU cc_start: 0.9572 (tp30) cc_final: 0.8877 (tp30) REVERT: P 27 ILE cc_start: 0.9188 (mt) cc_final: 0.8970 (mt) REVERT: P 55 PHE cc_start: 0.9003 (m-10) cc_final: 0.8279 (m-10) REVERT: P 59 LEU cc_start: 0.9471 (mm) cc_final: 0.9212 (mm) REVERT: P 62 PHE cc_start: 0.9246 (m-80) cc_final: 0.8903 (m-80) REVERT: P 64 LEU cc_start: 0.9650 (mt) cc_final: 0.9432 (mt) REVERT: P 68 PHE cc_start: 0.9325 (m-80) cc_final: 0.8843 (m-80) REVERT: Q 1 MET cc_start: 0.6321 (mmm) cc_final: 0.5921 (mmp) REVERT: Q 55 PHE cc_start: 0.9216 (m-10) cc_final: 0.8831 (m-80) REVERT: Q 68 PHE cc_start: 0.9117 (m-80) cc_final: 0.8676 (m-80) REVERT: T 249 ARG cc_start: 0.9306 (ptp-170) cc_final: 0.9049 (ptt-90) REVERT: T 264 MET cc_start: 0.9048 (mmt) cc_final: 0.8690 (tpt) REVERT: T 282 PHE cc_start: 0.9014 (t80) cc_final: 0.8710 (t80) REVERT: T 286 ILE cc_start: 0.9440 (pt) cc_final: 0.9205 (pt) REVERT: Z 84 MET cc_start: 0.9339 (tpp) cc_final: 0.8992 (tpp) REVERT: Z 206 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9089 (mm-30) REVERT: Z 264 MET cc_start: 0.9322 (mmm) cc_final: 0.9098 (mmm) REVERT: Z 280 GLU cc_start: 0.9381 (tm-30) cc_final: 0.8929 (tm-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2044 time to fit residues: 110.4315 Evaluate side-chains 289 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062068 restraints weight = 90168.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.063298 restraints weight = 63358.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064091 restraints weight = 48995.698| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13182 Z= 0.163 Angle : 0.673 10.558 17946 Z= 0.358 Chirality : 0.045 0.478 2226 Planarity : 0.005 0.066 2320 Dihedral : 3.889 17.175 1945 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 1.57 (0.19), residues: 1830 helix: 1.58 (0.13), residues: 1503 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 208 HIS 0.001 0.000 HIS V 149 PHE 0.044 0.002 PHE O 62 TYR 0.031 0.002 TYR Z 277 ARG 0.006 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1284) hydrogen bonds : angle 3.98153 ( 3831) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.50635 ( 4) covalent geometry : bond 0.00363 (13180) covalent geometry : angle 0.67333 (17942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.42 seconds wall clock time: 82 minutes 47.09 seconds (4967.09 seconds total)