Starting phenix.real_space_refine on Wed Jun 11 13:43:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itw_60881/06_2025/9itw_60881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itw_60881/06_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_60881/06_2025/9itw_60881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itw_60881/06_2025/9itw_60881.map" model { file = "/net/cci-nas-00/data/ceres_data/9itw_60881/06_2025/9itw_60881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itw_60881/06_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-5710/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: 8.57, per 1000 atoms: 0.66 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: 3.35 Conformation dependent library (CDL) restraints added in 2.0 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: 1.06 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: 3.63 Time building geometry restraints manager: 3.93 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: 5.200 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.500 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- 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 : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2218 time to fit residues: 167.1031 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 : 1.300 ------------------------------------------------------------------------------- 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 = 0.063670 restraints weight = 84840.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.064949 restraints weight = 59061.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.065809 restraints weight = 45276.779| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- 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 0.47840 ( 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 : 1.476 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: 0.7495 (tpt) cc_final: 0.7228 (tpt) REVERT: V 34 MET cc_start: 0.9012 (tpt) cc_final: 0.8632 (tmm) REVERT: V 38 ASN cc_start: 0.9263 (m-40) cc_final: 0.8689 (m-40) REVERT: V 89 GLN cc_start: 0.9446 (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: 0.8606 (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: 0.9206 (t) cc_final: 0.8957 (m) REVERT: I 48 TYR cc_start: 0.9043 (m-80) cc_final: 0.8187 (m-80) REVERT: I 49 MET cc_start: 0.9241 (ttp) cc_final: 0.8670 (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: 0.8532 (m-80) REVERT: K 57 GLU cc_start: 0.9399 (tp30) cc_final: 0.8735 (pt0) REVERT: L 15 LEU cc_start: 0.9158 (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: 0.9532 (mt) REVERT: L 29 SER cc_start: 0.9628 (t) cc_final: 0.9341 (p) REVERT: L 33 GLN cc_start: 0.9427 (tt0) cc_final: 0.9143 (mm110) REVERT: L 48 TYR cc_start: 0.8850 (m-80) cc_final: 0.8021 (m-80) REVERT: L 57 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8335 (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: 0.8815 (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: 0.8378 (mt-10) cc_final: 0.8024 (pt0) REVERT: N 59 LEU cc_start: 0.9379 (mm) cc_final: 0.9141 (mm) REVERT: N 62 PHE cc_start: 0.9370 (m-10) cc_final: 0.9046 (m-80) REVERT: N 66 ILE cc_start: 0.9338 (mm) cc_final: 0.9085 (mm) REVERT: O 1 MET cc_start: 0.6870 (tpt) cc_final: 0.6556 (tpt) REVERT: O 57 GLU cc_start: 0.9484 (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: 0.9335 (Cg_exo) cc_final: 0.9070 (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: 0.9083 (mm-40) REVERT: P 53 ILE cc_start: 0.9399 (pt) cc_final: 0.8868 (pt) REVERT: P 56 THR cc_start: 0.9087 (p) cc_final: 0.8222 (p) REVERT: P 57 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9103 (mm-30) REVERT: P 59 LEU cc_start: 0.9439 (mm) cc_final: 0.9132 (mm) REVERT: P 62 PHE cc_start: 0.9125 (m-10) cc_final: 0.8846 (m-80) REVERT: P 64 LEU cc_start: 0.9716 (mt) cc_final: 0.9435 (mt) REVERT: Q 1 MET cc_start: 0.6395 (mmm) cc_final: 0.6036 (mmm) REVERT: Q 68 PHE cc_start: 0.9069 (m-80) cc_final: 0.8733 (m-80) REVERT: T 244 PHE cc_start: 0.9139 (m-80) cc_final: 0.8731 (m-80) REVERT: T 264 MET cc_start: 0.9081 (mmt) cc_final: 0.8703 (tpp) REVERT: T 269 PRO cc_start: -0.4013 (Cg_endo) cc_final: -0.4282 (Cg_exo) REVERT: T 273 PRO cc_start: 0.5729 (Cg_exo) cc_final: 0.4758 (Cg_exo) REVERT: Z 89 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8029 (tm-30) REVERT: Z 125 LEU cc_start: 0.9189 (mp) cc_final: 0.8101 (mp) REVERT: Z 206 GLU cc_start: 0.9292 (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: 0.9479 (p) cc_final: 0.8971 (p) outliers start: 2 outliers final: 1 residues processed: 424 average time/residue: 0.2061 time to fit residues: 132.3615 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 : 1.316 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 157 optimal weight: 0.0170 chunk 162 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.079594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062786 restraints weight = 85286.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064111 restraints weight = 59260.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.065015 restraints weight = 45590.550| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3228 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= 0.152 Angle : 0.576 10.020 17946 Z= 0.309 Chirality : 0.041 0.197 2226 Planarity : 0.004 0.053 2320 Dihedral : 3.790 18.219 1945 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 1.64 (0.19), residues: 1830 helix: 1.68 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.50 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.003 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 0.04774 ( 1284) hydrogen bonds : angle 3.88231 ( 3831) SS BOND : bond 0.00050 ( 2) SS BOND : angle 0.25588 ( 4) covalent geometry : bond 0.00320 (13180) covalent geometry : angle 0.57648 (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 402 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 398 time to evaluate : 1.325 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: Y 33 VAL cc_start: 0.9558 (t) cc_final: 0.9301 (p) REVERT: Y 34 MET cc_start: 0.9114 (mmp) cc_final: 0.8613 (mmm) REVERT: Y 90 GLN cc_start: 0.9030 (mp10) cc_final: 0.8794 (mp10) REVERT: Y 132 VAL cc_start: 0.9556 (p) cc_final: 0.9257 (m) REVERT: V 25 LEU cc_start: 0.9626 (mt) cc_final: 0.9384 (mt) REVERT: V 34 MET cc_start: 0.8986 (tpt) cc_final: 0.8557 (tmm) REVERT: V 38 ASN cc_start: 0.9275 (m-40) cc_final: 0.8716 (m110) REVERT: H 50 PHE cc_start: 0.8948 (m-80) cc_final: 0.8636 (m-10) REVERT: H 51 ILE cc_start: 0.9434 (mt) cc_final: 0.9126 (mt) REVERT: H 53 ILE cc_start: 0.9094 (tp) cc_final: 0.8626 (tp) REVERT: H 55 PHE cc_start: 0.8909 (m-80) cc_final: 0.8557 (m-80) REVERT: H 57 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8514 (pt0) REVERT: I 48 TYR cc_start: 0.8963 (m-80) cc_final: 0.8185 (m-80) REVERT: I 49 MET cc_start: 0.9165 (ttp) cc_final: 0.8712 (tmm) REVERT: J 35 ILE cc_start: 0.8818 (mm) cc_final: 0.8539 (tp) REVERT: K 1 MET cc_start: 0.6419 (tpp) cc_final: 0.6109 (tpp) REVERT: K 20 PRO cc_start: 0.9444 (Cg_exo) cc_final: 0.9187 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9179 (m-10) cc_final: 0.8669 (m-80) REVERT: K 53 ILE cc_start: 0.9468 (mm) cc_final: 0.9176 (mm) REVERT: K 57 GLU cc_start: 0.9362 (tp30) cc_final: 0.8833 (pt0) REVERT: L 15 LEU cc_start: 0.9206 (mt) cc_final: 0.8962 (tp) REVERT: L 24 ILE cc_start: 0.9403 (mt) cc_final: 0.9128 (mm) REVERT: L 26 ILE cc_start: 0.9776 (mt) cc_final: 0.9477 (tt) REVERT: L 29 SER cc_start: 0.9632 (t) cc_final: 0.9269 (p) REVERT: L 33 GLN cc_start: 0.9439 (tt0) cc_final: 0.9117 (mm110) REVERT: L 48 TYR cc_start: 0.8906 (m-80) cc_final: 0.7891 (m-80) REVERT: L 49 MET cc_start: 0.9419 (ppp) cc_final: 0.9187 (tmm) REVERT: L 57 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8309 (pt0) REVERT: L 62 PHE cc_start: 0.8752 (m-10) cc_final: 0.8484 (m-80) REVERT: M 41 ILE cc_start: 0.8766 (tp) cc_final: 0.8289 (tt) REVERT: N 43 ASN cc_start: 0.8981 (p0) cc_final: 0.8712 (p0) REVERT: N 51 ILE cc_start: 0.9467 (mt) cc_final: 0.9069 (tt) REVERT: N 55 PHE cc_start: 0.9404 (m-10) cc_final: 0.9104 (m-80) REVERT: N 64 LEU cc_start: 0.9392 (mt) cc_final: 0.9034 (mt) REVERT: N 66 ILE cc_start: 0.9333 (mm) cc_final: 0.9061 (mm) REVERT: O 57 GLU cc_start: 0.9460 (tp30) cc_final: 0.8915 (tp30) REVERT: O 59 LEU cc_start: 0.9559 (mt) cc_final: 0.9357 (mp) REVERT: O 62 PHE cc_start: 0.9376 (m-10) cc_final: 0.9164 (m-80) REVERT: P 11 LEU cc_start: 0.9570 (mm) cc_final: 0.9295 (mm) REVERT: P 20 PRO cc_start: 0.9294 (Cg_exo) cc_final: 0.9091 (Cg_endo) REVERT: P 33 GLN cc_start: 0.9568 (mt0) cc_final: 0.9064 (mm-40) REVERT: P 57 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9294 (mm-30) REVERT: P 59 LEU cc_start: 0.9474 (mm) cc_final: 0.9163 (mm) REVERT: Q 1 MET cc_start: 0.6595 (mmm) cc_final: 0.6052 (mmm) REVERT: Q 50 PHE cc_start: 0.9371 (m-80) cc_final: 0.8992 (m-80) REVERT: Q 55 PHE cc_start: 0.9090 (m-10) cc_final: 0.8811 (m-80) REVERT: Q 68 PHE cc_start: 0.9005 (m-80) cc_final: 0.8696 (m-80) REVERT: T 244 PHE cc_start: 0.9110 (m-80) cc_final: 0.8790 (m-80) REVERT: T 264 MET cc_start: 0.9047 (mmt) cc_final: 0.8604 (tpp) REVERT: T 273 PRO cc_start: 0.6036 (Cg_exo) cc_final: 0.5136 (Cg_exo) REVERT: Z 89 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7944 (tm-30) REVERT: Z 125 LEU cc_start: 0.9148 (mp) cc_final: 0.7941 (mp) REVERT: Z 206 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8929 (mm-30) REVERT: Z 280 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8737 (tm-30) REVERT: Z 281 VAL cc_start: 0.9413 (p) cc_final: 0.8908 (p) outliers start: 4 outliers final: 2 residues processed: 401 average time/residue: 0.2120 time to fit residues: 128.7493 Evaluate side-chains 332 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 115 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.079062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.062431 restraints weight = 88521.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.063734 restraints weight = 61581.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064605 restraints weight = 47362.539| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13182 Z= 0.169 Angle : 0.597 7.606 17946 Z= 0.320 Chirality : 0.043 0.544 2226 Planarity : 0.005 0.058 2320 Dihedral : 3.797 17.828 1945 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.27 % Allowed : 3.92 % Favored : 95.81 % 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: 1.50 (0.19), residues: 1830 helix: 1.56 (0.13), residues: 1489 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.039 0.002 PHE I 62 TYR 0.011 0.001 TYR H 48 ARG 0.019 0.001 ARG Y 119 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 1284) hydrogen bonds : angle 3.90676 ( 3831) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.37425 ( 4) covalent geometry : bond 0.00357 (13180) covalent geometry : angle 0.59714 (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 385 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 382 time to evaluate : 1.290 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: Y 34 MET cc_start: 0.9227 (mmp) cc_final: 0.8727 (mmm) REVERT: Y 105 LEU cc_start: 0.9604 (mp) cc_final: 0.9382 (mm) REVERT: Y 115 GLN cc_start: 0.9072 (pt0) cc_final: 0.8860 (pp30) REVERT: Y 119 ARG cc_start: 0.9221 (mpp-170) cc_final: 0.8975 (ptp-110) REVERT: V 34 MET cc_start: 0.9129 (tpt) cc_final: 0.8801 (tmm) REVERT: H 50 PHE cc_start: 0.8911 (m-80) cc_final: 0.8615 (m-10) REVERT: H 53 ILE cc_start: 0.9008 (tp) cc_final: 0.8534 (tp) REVERT: H 55 PHE cc_start: 0.8962 (m-80) cc_final: 0.8720 (m-80) REVERT: H 57 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8568 (pt0) REVERT: I 29 SER cc_start: 0.9281 (t) cc_final: 0.9052 (p) REVERT: I 48 TYR cc_start: 0.9027 (m-80) cc_final: 0.8142 (m-80) REVERT: I 49 MET cc_start: 0.9090 (ttp) cc_final: 0.8615 (tmm) REVERT: K 20 PRO cc_start: 0.9380 (Cg_exo) cc_final: 0.9163 (Cg_endo) REVERT: K 53 ILE cc_start: 0.9469 (mm) cc_final: 0.8926 (tp) REVERT: K 57 GLU cc_start: 0.9364 (tp30) cc_final: 0.8786 (pt0) REVERT: L 24 ILE cc_start: 0.9397 (mt) cc_final: 0.9063 (mm) REVERT: L 26 ILE cc_start: 0.9766 (mt) cc_final: 0.9463 (tt) REVERT: L 29 SER cc_start: 0.9611 (t) cc_final: 0.9280 (p) REVERT: L 33 GLN cc_start: 0.9441 (tt0) cc_final: 0.9071 (mm110) REVERT: L 48 TYR cc_start: 0.8855 (m-80) cc_final: 0.7811 (m-80) REVERT: L 57 GLU cc_start: 0.9375 (mm-30) cc_final: 0.8170 (pt0) REVERT: L 62 PHE cc_start: 0.8825 (m-10) cc_final: 0.8499 (m-80) REVERT: M 41 ILE cc_start: 0.8786 (tp) cc_final: 0.8311 (tt) REVERT: M 56 THR cc_start: 0.9299 (t) cc_final: 0.9099 (p) REVERT: N 43 ASN cc_start: 0.8993 (p0) cc_final: 0.8711 (p0) REVERT: N 51 ILE cc_start: 0.9472 (mt) cc_final: 0.9110 (tt) REVERT: N 55 PHE cc_start: 0.9424 (m-10) cc_final: 0.9160 (m-80) REVERT: N 57 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8312 (mt-10) REVERT: N 62 PHE cc_start: 0.9392 (m-10) cc_final: 0.9047 (m-80) REVERT: N 66 ILE cc_start: 0.9343 (mm) cc_final: 0.9105 (mm) REVERT: O 57 GLU cc_start: 0.9496 (tp30) cc_final: 0.8921 (tp30) REVERT: O 59 LEU cc_start: 0.9594 (mt) cc_final: 0.9359 (mp) REVERT: P 20 PRO cc_start: 0.9318 (Cg_exo) cc_final: 0.8969 (Cg_endo) REVERT: P 33 GLN cc_start: 0.9597 (mt0) cc_final: 0.9140 (mm-40) REVERT: P 53 ILE cc_start: 0.9482 (pt) cc_final: 0.9244 (pt) REVERT: P 56 THR cc_start: 0.9242 (p) cc_final: 0.8714 (t) REVERT: P 57 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9204 (mm-30) REVERT: P 64 LEU cc_start: 0.9738 (mt) cc_final: 0.9391 (mt) REVERT: P 68 PHE cc_start: 0.9246 (m-80) cc_final: 0.8570 (m-80) REVERT: Q 1 MET cc_start: 0.6588 (mmm) cc_final: 0.5958 (mmm) REVERT: Q 18 ILE cc_start: 0.8913 (mt) cc_final: 0.8696 (mt) REVERT: Q 50 PHE cc_start: 0.9411 (m-80) cc_final: 0.9164 (m-80) REVERT: Q 53 ILE cc_start: 0.8640 (mt) cc_final: 0.8350 (mt) REVERT: Q 55 PHE cc_start: 0.9130 (m-10) cc_final: 0.8892 (m-80) REVERT: Q 57 GLU cc_start: 0.9166 (pm20) cc_final: 0.8814 (pm20) REVERT: Q 68 PHE cc_start: 0.9127 (m-80) cc_final: 0.8723 (m-80) REVERT: T 244 PHE cc_start: 0.9152 (m-80) cc_final: 0.8866 (m-80) REVERT: T 264 MET cc_start: 0.9063 (mmt) cc_final: 0.8718 (tpp) REVERT: Z 84 MET cc_start: 0.9271 (tpp) cc_final: 0.8895 (tpp) REVERT: Z 125 LEU cc_start: 0.9194 (mp) cc_final: 0.7763 (mp) REVERT: Z 206 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9057 (mm-30) REVERT: Z 217 TYR cc_start: 0.7058 (t80) cc_final: 0.6842 (t80) REVERT: Z 280 GLU cc_start: 0.9353 (tm-30) cc_final: 0.8752 (tm-30) REVERT: Z 281 VAL cc_start: 0.9503 (p) cc_final: 0.8941 (p) outliers start: 3 outliers final: 2 residues processed: 384 average time/residue: 0.2036 time to fit residues: 118.2904 Evaluate side-chains 328 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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: 30.0000 chunk 163 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 146 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 92 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 33 GLN T 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.079923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.063022 restraints weight = 89848.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.064405 restraints weight = 61766.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065160 restraints weight = 46901.812| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13182 Z= 0.146 Angle : 0.587 8.223 17946 Z= 0.312 Chirality : 0.042 0.397 2226 Planarity : 0.004 0.059 2320 Dihedral : 3.782 16.850 1945 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % 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: 1.50 (0.19), residues: 1830 helix: 1.56 (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 0.008 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 136 PHE 0.026 0.001 PHE P 62 TYR 0.012 0.001 TYR K 48 ARG 0.004 0.000 ARG T 249 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 1284) hydrogen bonds : angle 3.79935 ( 3831) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.47641 ( 4) covalent geometry : bond 0.00316 (13180) covalent geometry : angle 0.58681 (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 386 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 1.492 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: Y 34 MET cc_start: 0.9151 (mmp) cc_final: 0.8723 (mmm) REVERT: Y 90 GLN cc_start: 0.9104 (mp10) cc_final: 0.8773 (mp10) REVERT: V 34 MET cc_start: 0.9037 (tpt) cc_final: 0.8778 (tmm) REVERT: H 50 PHE cc_start: 0.8917 (m-80) cc_final: 0.8591 (m-10) REVERT: H 53 ILE cc_start: 0.9040 (tp) cc_final: 0.8496 (tp) REVERT: H 55 PHE cc_start: 0.8971 (m-80) cc_final: 0.8663 (m-80) REVERT: H 57 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8558 (pt0) REVERT: I 29 SER cc_start: 0.9296 (t) cc_final: 0.9038 (p) REVERT: I 48 TYR cc_start: 0.9030 (m-80) cc_final: 0.8157 (m-80) REVERT: I 49 MET cc_start: 0.9193 (ttp) cc_final: 0.8840 (tmm) REVERT: K 20 PRO cc_start: 0.9397 (Cg_exo) cc_final: 0.9174 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9442 (m-80) cc_final: 0.8898 (m-80) REVERT: K 53 ILE cc_start: 0.9497 (mm) cc_final: 0.8827 (tp) REVERT: K 57 GLU cc_start: 0.9325 (tp30) cc_final: 0.8751 (pt0) REVERT: L 15 LEU cc_start: 0.9253 (tp) cc_final: 0.8947 (tp) REVERT: L 24 ILE cc_start: 0.9387 (mt) cc_final: 0.9017 (mm) REVERT: L 26 ILE cc_start: 0.9776 (mt) cc_final: 0.9455 (tt) REVERT: L 29 SER cc_start: 0.9588 (t) cc_final: 0.9278 (p) REVERT: L 33 GLN cc_start: 0.9442 (tt0) cc_final: 0.9050 (mm110) REVERT: L 41 ILE cc_start: 0.9001 (tp) cc_final: 0.8798 (tp) REVERT: L 48 TYR cc_start: 0.8785 (m-80) cc_final: 0.7756 (m-80) REVERT: L 57 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8178 (pt0) REVERT: L 62 PHE cc_start: 0.8763 (m-10) cc_final: 0.8484 (m-80) REVERT: M 41 ILE cc_start: 0.8804 (tp) cc_final: 0.8347 (tt) REVERT: N 43 ASN cc_start: 0.8964 (p0) cc_final: 0.8696 (p0) REVERT: N 51 ILE cc_start: 0.9418 (mt) cc_final: 0.8838 (tt) REVERT: N 55 PHE cc_start: 0.9354 (m-10) cc_final: 0.8935 (m-80) REVERT: N 62 PHE cc_start: 0.9332 (m-10) cc_final: 0.9070 (m-80) REVERT: N 66 ILE cc_start: 0.9319 (mm) cc_final: 0.9070 (mm) REVERT: O 50 PHE cc_start: 0.9138 (m-10) cc_final: 0.8888 (m-80) REVERT: O 57 GLU cc_start: 0.9498 (tp30) cc_final: 0.8844 (tp30) REVERT: O 62 PHE cc_start: 0.9179 (m-80) cc_final: 0.8899 (m-80) REVERT: P 20 PRO cc_start: 0.9336 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: P 53 ILE cc_start: 0.9447 (pt) cc_final: 0.9245 (pt) REVERT: P 56 THR cc_start: 0.9149 (p) cc_final: 0.8689 (t) REVERT: P 57 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9225 (mm-30) REVERT: P 62 PHE cc_start: 0.9267 (m-80) cc_final: 0.8919 (m-80) REVERT: P 64 LEU cc_start: 0.9687 (mt) cc_final: 0.9432 (mt) REVERT: Q 1 MET cc_start: 0.6351 (mmm) cc_final: 0.5712 (mmm) REVERT: Q 18 ILE cc_start: 0.8843 (mt) cc_final: 0.8534 (mt) REVERT: Q 50 PHE cc_start: 0.9400 (m-80) cc_final: 0.9179 (m-80) REVERT: Q 53 ILE cc_start: 0.8585 (mt) cc_final: 0.8176 (mt) REVERT: Q 68 PHE cc_start: 0.9058 (m-80) cc_final: 0.8684 (m-80) REVERT: T 244 PHE cc_start: 0.9109 (m-80) cc_final: 0.8815 (m-80) REVERT: T 264 MET cc_start: 0.9049 (mmt) cc_final: 0.8711 (tpp) REVERT: Z 206 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9039 (mm-30) REVERT: Z 280 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8664 (tp30) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2239 time to fit residues: 131.5252 Evaluate side-chains 315 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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: 0.8980 chunk 108 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 115 GLN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.078582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.062237 restraints weight = 86621.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063439 restraints weight = 61213.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.064272 restraints weight = 48055.154| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13182 Z= 0.168 Angle : 0.609 8.506 17946 Z= 0.327 Chirality : 0.043 0.382 2226 Planarity : 0.005 0.060 2320 Dihedral : 3.813 18.412 1945 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.09 % Allowed : 1.37 % Favored : 98.54 % 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: 1.33 (0.19), residues: 1830 helix: 1.45 (0.13), residues: 1473 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.038 0.002 PHE I 62 TYR 0.012 0.001 TYR H 48 ARG 0.012 0.001 ARG Y 119 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 1284) hydrogen bonds : angle 3.90884 ( 3831) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.42695 ( 4) covalent geometry : bond 0.00364 (13180) covalent geometry : angle 0.60911 (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 369 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 1.395 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: 0.9142 (mmp) cc_final: 0.8753 (mmm) REVERT: Y 115 GLN cc_start: 0.9660 (mp10) cc_final: 0.9244 (pm20) REVERT: Y 119 ARG cc_start: 0.9609 (ptp90) cc_final: 0.9391 (ptt-90) REVERT: V 21 LEU cc_start: 0.9573 (tp) cc_final: 0.9294 (tt) REVERT: V 25 LEU cc_start: 0.9667 (mt) cc_final: 0.9415 (mt) REVERT: H 50 PHE cc_start: 0.8865 (m-80) cc_final: 0.8562 (m-10) REVERT: H 51 ILE cc_start: 0.9435 (mt) cc_final: 0.9139 (mt) REVERT: H 55 PHE cc_start: 0.9051 (m-80) cc_final: 0.8703 (m-80) REVERT: I 1 MET cc_start: 0.8045 (mtp) cc_final: 0.7803 (mtp) REVERT: I 48 TYR cc_start: 0.9071 (m-80) cc_final: 0.8226 (m-80) REVERT: I 49 MET cc_start: 0.9210 (ttp) cc_final: 0.8807 (tmm) REVERT: K 20 PRO cc_start: 0.9393 (Cg_exo) cc_final: 0.9166 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9466 (m-80) cc_final: 0.8952 (m-80) REVERT: K 53 ILE cc_start: 0.9541 (mm) cc_final: 0.8816 (tp) REVERT: K 57 GLU cc_start: 0.9345 (tp30) cc_final: 0.8749 (pt0) REVERT: L 15 LEU cc_start: 0.9267 (tp) cc_final: 0.8949 (tp) REVERT: L 24 ILE cc_start: 0.9374 (mt) cc_final: 0.9170 (mm) REVERT: L 26 ILE cc_start: 0.9761 (mt) cc_final: 0.9461 (tt) REVERT: L 29 SER cc_start: 0.9589 (t) cc_final: 0.9262 (p) REVERT: L 33 GLN cc_start: 0.9448 (tt0) cc_final: 0.9078 (mm110) REVERT: L 48 TYR cc_start: 0.8850 (m-80) cc_final: 0.8014 (m-80) REVERT: L 56 THR cc_start: 0.9275 (t) cc_final: 0.9036 (t) REVERT: L 62 PHE cc_start: 0.8821 (m-10) cc_final: 0.8554 (m-80) REVERT: M 41 ILE cc_start: 0.8919 (tp) cc_final: 0.8462 (tt) REVERT: N 1 MET cc_start: 0.6486 (mtp) cc_final: 0.6246 (mtp) REVERT: N 43 ASN cc_start: 0.8988 (p0) cc_final: 0.8721 (p0) REVERT: N 51 ILE cc_start: 0.9400 (mt) cc_final: 0.8833 (tt) REVERT: N 55 PHE cc_start: 0.9351 (m-10) cc_final: 0.8940 (m-80) REVERT: N 62 PHE cc_start: 0.9376 (m-10) cc_final: 0.9145 (m-80) REVERT: N 66 ILE cc_start: 0.9331 (mm) cc_final: 0.9096 (mm) REVERT: O 50 PHE cc_start: 0.9268 (m-10) cc_final: 0.8900 (m-80) REVERT: O 57 GLU cc_start: 0.9514 (tp30) cc_final: 0.8947 (tp30) REVERT: O 62 PHE cc_start: 0.9181 (m-80) cc_final: 0.8893 (m-80) REVERT: P 20 PRO cc_start: 0.9309 (Cg_exo) cc_final: 0.8990 (Cg_endo) REVERT: P 56 THR cc_start: 0.9126 (p) cc_final: 0.8646 (t) REVERT: P 57 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9216 (mm-30) REVERT: P 59 LEU cc_start: 0.9493 (mm) cc_final: 0.9279 (mm) REVERT: P 62 PHE cc_start: 0.9301 (m-80) cc_final: 0.8940 (m-80) REVERT: P 68 PHE cc_start: 0.9307 (m-80) cc_final: 0.9102 (m-80) REVERT: Q 1 MET cc_start: 0.6433 (mmm) cc_final: 0.5819 (mmm) REVERT: Q 50 PHE cc_start: 0.9418 (m-80) cc_final: 0.9151 (m-80) REVERT: Q 68 PHE cc_start: 0.9117 (m-80) cc_final: 0.8697 (m-80) REVERT: T 244 PHE cc_start: 0.9139 (m-80) cc_final: 0.8882 (m-80) REVERT: T 264 MET cc_start: 0.9032 (mmt) cc_final: 0.8800 (tpp) REVERT: Z 84 MET cc_start: 0.9336 (tpp) cc_final: 0.9093 (tpp) REVERT: Z 125 LEU cc_start: 0.9235 (mp) cc_final: 0.8895 (mm) REVERT: Z 206 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9043 (mm-30) REVERT: Z 235 GLU cc_start: 0.8520 (pt0) cc_final: 0.8313 (pt0) REVERT: Z 280 GLU cc_start: 0.9286 (tm-30) cc_final: 0.8747 (tm-30) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.2137 time to fit residues: 120.0275 Evaluate side-chains 300 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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: 0.8980 chunk 163 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Z 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.079610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062323 restraints weight = 86464.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063601 restraints weight = 61171.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.064423 restraints weight = 47691.090| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13182 Z= 0.149 Angle : 0.601 9.185 17946 Z= 0.322 Chirality : 0.043 0.354 2226 Planarity : 0.005 0.062 2320 Dihedral : 3.755 16.217 1945 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 1.54 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 136 PHE 0.030 0.001 PHE Q 62 TYR 0.012 0.001 TYR Z 277 ARG 0.011 0.000 ARG V 99 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 1284) hydrogen bonds : angle 3.82002 ( 3831) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.46612 ( 4) covalent geometry : bond 0.00320 (13180) covalent geometry : angle 0.60144 (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 369 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.361 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: 0.9078 (mmp) cc_final: 0.8722 (mmm) REVERT: Y 90 GLN cc_start: 0.9010 (mp10) cc_final: 0.8798 (mp10) REVERT: Y 115 GLN cc_start: 0.9646 (mp10) cc_final: 0.9204 (pt0) REVERT: Y 119 ARG cc_start: 0.9581 (ptp90) cc_final: 0.9329 (ptt-90) REVERT: V 21 LEU cc_start: 0.9523 (tp) cc_final: 0.9258 (tt) REVERT: V 25 LEU cc_start: 0.9587 (mt) cc_final: 0.9333 (mt) REVERT: V 82 GLN cc_start: 0.9398 (tp-100) cc_final: 0.9149 (tp-100) REVERT: X 18 PHE cc_start: 0.3411 (t80) cc_final: 0.3126 (m-80) REVERT: X 21 LEU cc_start: 0.7820 (pp) cc_final: 0.7587 (pp) REVERT: H 29 SER cc_start: 0.9390 (t) cc_final: 0.9135 (m) REVERT: H 50 PHE cc_start: 0.8866 (m-80) cc_final: 0.8597 (m-10) REVERT: H 51 ILE cc_start: 0.9388 (mt) cc_final: 0.9093 (mt) REVERT: H 55 PHE cc_start: 0.8956 (m-80) cc_final: 0.8634 (m-80) REVERT: I 29 SER cc_start: 0.9330 (t) cc_final: 0.9056 (p) REVERT: I 49 MET cc_start: 0.9219 (ttp) cc_final: 0.8860 (tmm) REVERT: J 1 MET cc_start: 0.7376 (mmt) cc_final: 0.7162 (mpp) REVERT: K 20 PRO cc_start: 0.9441 (Cg_exo) cc_final: 0.9219 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9428 (m-80) cc_final: 0.9003 (m-80) REVERT: K 53 ILE cc_start: 0.9380 (mm) cc_final: 0.8779 (tp) REVERT: K 57 GLU cc_start: 0.9278 (tp30) cc_final: 0.8677 (pt0) REVERT: L 15 LEU cc_start: 0.9355 (tp) cc_final: 0.9067 (tp) REVERT: L 26 ILE cc_start: 0.9782 (mt) cc_final: 0.9482 (tt) REVERT: L 29 SER cc_start: 0.9588 (t) cc_final: 0.9300 (p) REVERT: L 33 GLN cc_start: 0.9455 (tt0) cc_final: 0.9116 (mm110) REVERT: L 48 TYR cc_start: 0.8781 (m-80) cc_final: 0.7949 (m-80) REVERT: L 62 PHE cc_start: 0.8669 (m-10) cc_final: 0.8447 (m-80) REVERT: M 41 ILE cc_start: 0.8902 (tp) cc_final: 0.8434 (tt) REVERT: N 43 ASN cc_start: 0.8997 (p0) cc_final: 0.8721 (p0) REVERT: N 51 ILE cc_start: 0.9358 (mt) cc_final: 0.8747 (tt) REVERT: N 55 PHE cc_start: 0.9271 (m-10) cc_final: 0.8846 (m-80) REVERT: N 62 PHE cc_start: 0.9319 (m-10) cc_final: 0.9066 (m-80) REVERT: N 66 ILE cc_start: 0.9328 (mm) cc_final: 0.9082 (mm) REVERT: O 40 GLU cc_start: 0.9291 (mp0) cc_final: 0.9081 (pp20) REVERT: O 50 PHE cc_start: 0.9180 (m-10) cc_final: 0.8859 (m-80) REVERT: O 57 GLU cc_start: 0.9547 (tp30) cc_final: 0.8841 (tp30) REVERT: P 27 ILE cc_start: 0.9138 (mt) cc_final: 0.8915 (mt) REVERT: P 53 ILE cc_start: 0.9423 (pt) cc_final: 0.9215 (pt) REVERT: P 55 PHE cc_start: 0.8995 (m-10) cc_final: 0.8157 (m-80) REVERT: P 57 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9213 (mm-30) REVERT: P 59 LEU cc_start: 0.9512 (mm) cc_final: 0.9246 (mm) REVERT: P 62 PHE cc_start: 0.9187 (m-80) cc_final: 0.8868 (m-80) REVERT: Q 1 MET cc_start: 0.6401 (mmm) cc_final: 0.5782 (mmm) REVERT: Q 57 GLU cc_start: 0.9117 (pm20) cc_final: 0.8624 (pm20) REVERT: Q 68 PHE cc_start: 0.8947 (m-80) cc_final: 0.8622 (m-80) REVERT: T 244 PHE cc_start: 0.9083 (m-80) cc_final: 0.8823 (m-80) REVERT: T 264 MET cc_start: 0.9014 (mmt) cc_final: 0.8748 (tpp) REVERT: T 282 PHE cc_start: 0.9055 (t80) cc_final: 0.8692 (t80) REVERT: T 286 ILE cc_start: 0.9459 (pt) cc_final: 0.9199 (pt) REVERT: Z 125 LEU cc_start: 0.9195 (mp) cc_final: 0.8886 (mm) REVERT: Z 206 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9019 (mm-30) REVERT: Z 235 GLU cc_start: 0.8437 (pt0) cc_final: 0.8222 (pt0) REVERT: Z 264 MET cc_start: 0.9297 (mmm) cc_final: 0.9013 (mmm) REVERT: Z 280 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8624 (tm-30) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2038 time to fit residues: 114.9453 Evaluate side-chains 309 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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: 1.9990 chunk 141 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.079500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062109 restraints weight = 86457.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.063373 restraints weight = 61348.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.064228 restraints weight = 47878.745| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13182 Z= 0.153 Angle : 0.632 10.999 17946 Z= 0.337 Chirality : 0.044 0.305 2226 Planarity : 0.005 0.062 2320 Dihedral : 3.783 17.045 1945 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: 1.36 (0.19), residues: 1830 helix: 1.46 (0.13), residues: 1489 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.001 0.000 HIS V 149 PHE 0.036 0.002 PHE I 62 TYR 0.012 0.001 TYR H 48 ARG 0.006 0.000 ARG V 99 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 1284) hydrogen bonds : angle 3.81996 ( 3831) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.46798 ( 4) covalent geometry : bond 0.00337 (13180) covalent geometry : angle 0.63236 (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 372 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9025 (mmp) cc_final: 0.8699 (mmm) REVERT: Y 104 ARG cc_start: 0.9010 (ttt-90) cc_final: 0.8722 (ttt90) REVERT: Y 115 GLN cc_start: 0.9649 (mp10) cc_final: 0.9126 (pt0) REVERT: Y 119 ARG cc_start: 0.9574 (ptp90) cc_final: 0.9287 (ptt-90) REVERT: V 21 LEU cc_start: 0.9520 (tp) cc_final: 0.9257 (tt) REVERT: V 25 LEU cc_start: 0.9564 (mt) cc_final: 0.9294 (mt) REVERT: X 18 PHE cc_start: 0.3662 (t80) cc_final: 0.3345 (m-80) REVERT: X 21 LEU cc_start: 0.7900 (pp) cc_final: 0.7686 (pp) REVERT: H 29 SER cc_start: 0.9397 (t) cc_final: 0.9139 (m) REVERT: H 49 MET cc_start: 0.9133 (ppp) cc_final: 0.8549 (ppp) REVERT: H 50 PHE cc_start: 0.8861 (m-80) cc_final: 0.8515 (m-10) REVERT: H 53 ILE cc_start: 0.9196 (tp) cc_final: 0.8742 (tp) REVERT: H 55 PHE cc_start: 0.8941 (m-80) cc_final: 0.8630 (m-80) REVERT: I 29 SER cc_start: 0.9327 (t) cc_final: 0.9072 (p) REVERT: I 49 MET cc_start: 0.9227 (ttp) cc_final: 0.8875 (tmm) REVERT: J 1 MET cc_start: 0.7378 (mmt) cc_final: 0.7109 (mpp) REVERT: K 48 TYR cc_start: 0.9435 (m-80) cc_final: 0.8998 (m-80) REVERT: K 49 MET cc_start: 0.9471 (ppp) cc_final: 0.9222 (ppp) REVERT: K 53 ILE cc_start: 0.9534 (mm) cc_final: 0.9225 (mm) REVERT: K 57 GLU cc_start: 0.9195 (tp30) cc_final: 0.8641 (pt0) REVERT: L 15 LEU cc_start: 0.9312 (tp) cc_final: 0.8995 (tp) REVERT: L 26 ILE cc_start: 0.9781 (mt) cc_final: 0.9465 (tt) REVERT: L 29 SER cc_start: 0.9599 (t) cc_final: 0.9319 (p) REVERT: L 33 GLN cc_start: 0.9460 (tt0) cc_final: 0.9125 (mm110) REVERT: L 64 LEU cc_start: 0.9331 (mt) cc_final: 0.9101 (mt) REVERT: M 41 ILE cc_start: 0.8929 (tp) cc_final: 0.8475 (tt) REVERT: N 43 ASN cc_start: 0.9013 (p0) cc_final: 0.8744 (p0) REVERT: N 51 ILE cc_start: 0.9353 (mt) cc_final: 0.8719 (tt) REVERT: N 55 PHE cc_start: 0.9238 (m-10) cc_final: 0.8769 (m-80) REVERT: N 66 ILE cc_start: 0.9334 (mm) cc_final: 0.9109 (mm) REVERT: O 40 GLU cc_start: 0.9333 (mp0) cc_final: 0.9126 (pp20) REVERT: O 50 PHE cc_start: 0.9151 (m-10) cc_final: 0.8843 (m-80) REVERT: O 57 GLU cc_start: 0.9548 (tp30) cc_final: 0.8889 (tp30) REVERT: P 27 ILE cc_start: 0.9157 (mt) cc_final: 0.8922 (mt) REVERT: P 57 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9207 (mm-30) REVERT: P 59 LEU cc_start: 0.9506 (mm) cc_final: 0.9246 (mm) REVERT: P 62 PHE cc_start: 0.9206 (m-80) cc_final: 0.8842 (m-80) REVERT: P 64 LEU cc_start: 0.9665 (mt) cc_final: 0.9361 (mt) REVERT: P 68 PHE cc_start: 0.9104 (m-80) cc_final: 0.8443 (m-80) REVERT: Q 1 MET cc_start: 0.6146 (mmm) cc_final: 0.5705 (mmp) REVERT: Q 50 PHE cc_start: 0.9402 (m-80) cc_final: 0.9183 (m-80) REVERT: Q 68 PHE cc_start: 0.8905 (m-80) cc_final: 0.8601 (m-80) REVERT: T 264 MET cc_start: 0.9003 (mmt) cc_final: 0.8730 (tpp) REVERT: Z 206 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9001 (mm-30) REVERT: Z 280 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8898 (tp30) REVERT: Z 286 ILE cc_start: 0.9837 (tp) cc_final: 0.9545 (tp) REVERT: Z 290 ILE cc_start: 0.9565 (mm) cc_final: 0.9285 (mm) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2063 time to fit residues: 117.4175 Evaluate side-chains 301 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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: 20.0000 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 40.0000 chunk 177 optimal weight: 4.9990 chunk 146 optimal weight: 0.0770 chunk 150 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.078440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061610 restraints weight = 89980.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062850 restraints weight = 63714.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.063666 restraints weight = 49302.904| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13182 Z= 0.182 Angle : 0.670 14.191 17946 Z= 0.358 Chirality : 0.046 0.341 2226 Planarity : 0.005 0.071 2320 Dihedral : 3.870 20.744 1945 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 1.36 (0.19), residues: 1830 helix: 1.51 (0.13), residues: 1477 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.035 0.002 PHE L 62 TYR 0.013 0.001 TYR Z 277 ARG 0.015 0.001 ARG T 249 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 1284) hydrogen bonds : angle 3.91954 ( 3831) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.39398 ( 4) covalent geometry : bond 0.00395 (13180) covalent geometry : angle 0.66976 (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 363 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.408 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: Y 34 MET cc_start: 0.9142 (mmp) cc_final: 0.8808 (mmm) REVERT: Y 115 GLN cc_start: 0.9667 (mp10) cc_final: 0.9236 (pt0) REVERT: Y 119 ARG cc_start: 0.9575 (ptp90) cc_final: 0.9309 (ptt-90) REVERT: V 25 LEU cc_start: 0.9637 (mt) cc_final: 0.9423 (mt) REVERT: V 82 GLN cc_start: 0.9483 (tp-100) cc_final: 0.9138 (tp-100) REVERT: H 29 SER cc_start: 0.9371 (t) cc_final: 0.9108 (m) REVERT: H 50 PHE cc_start: 0.8835 (m-80) cc_final: 0.8582 (m-10) REVERT: H 53 ILE cc_start: 0.9105 (tp) cc_final: 0.8480 (tp) REVERT: H 55 PHE cc_start: 0.9019 (m-80) cc_final: 0.8777 (m-80) REVERT: H 57 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8988 (mm-30) REVERT: I 29 SER cc_start: 0.9322 (t) cc_final: 0.9068 (p) REVERT: I 49 MET cc_start: 0.9253 (ttp) cc_final: 0.8857 (tmm) REVERT: K 48 TYR cc_start: 0.9452 (m-80) cc_final: 0.8762 (m-80) REVERT: K 53 ILE cc_start: 0.9501 (mm) cc_final: 0.8883 (tp) REVERT: K 57 GLU cc_start: 0.9239 (tp30) cc_final: 0.8644 (pt0) REVERT: L 15 LEU cc_start: 0.9307 (tp) cc_final: 0.8993 (tp) REVERT: L 26 ILE cc_start: 0.9769 (mt) cc_final: 0.9496 (tt) REVERT: L 29 SER cc_start: 0.9595 (t) cc_final: 0.9285 (p) REVERT: L 33 GLN cc_start: 0.9478 (tt0) cc_final: 0.9135 (mm110) REVERT: L 48 TYR cc_start: 0.9201 (m-80) cc_final: 0.8105 (m-80) REVERT: L 64 LEU cc_start: 0.9324 (mt) cc_final: 0.9120 (mt) REVERT: M 41 ILE cc_start: 0.8936 (tp) cc_final: 0.8468 (tt) REVERT: N 43 ASN cc_start: 0.8989 (p0) cc_final: 0.8721 (p0) REVERT: N 51 ILE cc_start: 0.9349 (mt) cc_final: 0.8876 (tt) REVERT: N 55 PHE cc_start: 0.9227 (m-10) cc_final: 0.8926 (m-80) REVERT: N 66 ILE cc_start: 0.9364 (mm) cc_final: 0.9143 (mm) REVERT: O 50 PHE cc_start: 0.9204 (m-10) cc_final: 0.8860 (m-80) REVERT: O 57 GLU cc_start: 0.9518 (tp30) cc_final: 0.8834 (tp30) REVERT: P 27 ILE cc_start: 0.9170 (mt) cc_final: 0.8956 (mt) REVERT: P 57 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9227 (mm-30) REVERT: P 59 LEU cc_start: 0.9507 (mm) cc_final: 0.9247 (mm) REVERT: P 62 PHE cc_start: 0.9246 (m-80) cc_final: 0.8880 (m-80) REVERT: P 64 LEU cc_start: 0.9681 (mt) cc_final: 0.9453 (mt) REVERT: Q 50 PHE cc_start: 0.9399 (m-80) cc_final: 0.9151 (m-80) REVERT: Q 68 PHE cc_start: 0.9050 (m-80) cc_final: 0.8657 (m-80) REVERT: T 264 MET cc_start: 0.9008 (mmt) cc_final: 0.8637 (tpt) REVERT: T 282 PHE cc_start: 0.9068 (t80) cc_final: 0.8783 (t80) REVERT: T 286 ILE cc_start: 0.9462 (pt) cc_final: 0.9229 (pt) REVERT: Z 206 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9028 (mm-30) REVERT: Z 264 MET cc_start: 0.9278 (mmm) cc_final: 0.9036 (mmm) REVERT: Z 280 GLU cc_start: 0.9326 (tm-30) cc_final: 0.8834 (tm-30) REVERT: Z 286 ILE cc_start: 0.9838 (tp) cc_final: 0.9553 (tp) REVERT: Z 290 ILE cc_start: 0.9623 (mm) cc_final: 0.9347 (mm) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2137 time to fit residues: 118.2504 Evaluate side-chains 300 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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: 0.6980 chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 Z 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.078346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061236 restraints weight = 87396.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062473 restraints weight = 62109.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063276 restraints weight = 48489.712| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13182 Z= 0.174 Angle : 0.670 10.387 17946 Z= 0.357 Chirality : 0.045 0.294 2226 Planarity : 0.005 0.066 2320 Dihedral : 3.914 16.852 1945 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: 1.31 (0.19), residues: 1830 helix: 1.44 (0.13), residues: 1475 sheet: None (None), residues: 0 loop : -1.49 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.036 0.002 PHE L 62 TYR 0.015 0.001 TYR H 48 ARG 0.008 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 1284) hydrogen bonds : angle 3.99690 ( 3831) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.39695 ( 4) covalent geometry : bond 0.00384 (13180) covalent geometry : angle 0.67037 (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 362 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.195 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: 0.9071 (mmp) cc_final: 0.8752 (mmm) REVERT: Y 115 GLN cc_start: 0.9668 (mp10) cc_final: 0.9155 (pt0) REVERT: Y 119 ARG cc_start: 0.9570 (ptp90) cc_final: 0.9223 (ptt-90) REVERT: V 84 GLN cc_start: 0.9112 (pt0) cc_final: 0.8850 (pt0) REVERT: H 29 SER cc_start: 0.9359 (t) cc_final: 0.9101 (m) REVERT: H 49 MET cc_start: 0.9181 (ppp) cc_final: 0.8648 (ppp) REVERT: H 50 PHE cc_start: 0.8865 (m-80) cc_final: 0.8567 (m-10) REVERT: H 53 ILE cc_start: 0.9170 (tp) cc_final: 0.8555 (tp) REVERT: H 55 PHE cc_start: 0.9211 (m-80) cc_final: 0.8907 (m-80) REVERT: H 57 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9016 (mm-30) REVERT: I 29 SER cc_start: 0.9343 (t) cc_final: 0.9096 (p) REVERT: I 49 MET cc_start: 0.9229 (ttp) cc_final: 0.9012 (tmm) REVERT: J 28 VAL cc_start: 0.9502 (t) cc_final: 0.9262 (m) REVERT: K 48 TYR cc_start: 0.9373 (m-80) cc_final: 0.8947 (m-80) REVERT: K 53 ILE cc_start: 0.9320 (mm) cc_final: 0.9073 (mm) REVERT: K 57 GLU cc_start: 0.9185 (tp30) cc_final: 0.8614 (pt0) REVERT: L 15 LEU cc_start: 0.9224 (tp) cc_final: 0.8915 (tp) REVERT: L 26 ILE cc_start: 0.9778 (mt) cc_final: 0.9479 (tt) REVERT: L 29 SER cc_start: 0.9614 (t) cc_final: 0.9338 (p) REVERT: L 33 GLN cc_start: 0.9464 (tt0) cc_final: 0.9140 (mm110) REVERT: L 48 TYR cc_start: 0.9189 (m-80) cc_final: 0.8180 (m-80) REVERT: L 62 PHE cc_start: 0.8715 (m-80) cc_final: 0.8509 (m-80) REVERT: L 64 LEU cc_start: 0.9302 (mt) cc_final: 0.8970 (mt) REVERT: M 41 ILE cc_start: 0.8912 (tp) cc_final: 0.8364 (tt) REVERT: N 43 ASN cc_start: 0.9015 (p0) cc_final: 0.8745 (p0) REVERT: N 51 ILE cc_start: 0.9346 (mt) cc_final: 0.8922 (tt) REVERT: N 55 PHE cc_start: 0.9163 (m-10) cc_final: 0.8897 (m-80) REVERT: N 66 ILE cc_start: 0.9358 (mm) cc_final: 0.9128 (mm) REVERT: O 50 PHE cc_start: 0.9165 (m-10) cc_final: 0.8842 (m-80) REVERT: O 57 GLU cc_start: 0.9488 (tp30) cc_final: 0.8801 (tp30) REVERT: P 27 ILE cc_start: 0.9164 (mt) cc_final: 0.8952 (mt) REVERT: P 55 PHE cc_start: 0.8999 (m-80) cc_final: 0.8176 (m-80) REVERT: P 57 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9247 (mm-30) REVERT: P 59 LEU cc_start: 0.9526 (mm) cc_final: 0.9239 (mm) REVERT: P 62 PHE cc_start: 0.9210 (m-80) cc_final: 0.8840 (m-80) REVERT: P 68 PHE cc_start: 0.9186 (m-80) cc_final: 0.8944 (m-80) REVERT: Q 1 MET cc_start: 0.8066 (tpt) cc_final: 0.7639 (tpp) REVERT: Q 50 PHE cc_start: 0.9392 (m-80) cc_final: 0.9134 (m-80) REVERT: Q 55 PHE cc_start: 0.9196 (m-80) cc_final: 0.8724 (m-80) REVERT: Q 68 PHE cc_start: 0.8998 (m-80) cc_final: 0.8615 (m-80) REVERT: T 244 PHE cc_start: 0.9125 (m-80) cc_final: 0.8876 (m-80) REVERT: T 264 MET cc_start: 0.9023 (mmt) cc_final: 0.8659 (tpt) REVERT: T 282 PHE cc_start: 0.9037 (t80) cc_final: 0.8746 (t80) REVERT: T 286 ILE cc_start: 0.9437 (pt) cc_final: 0.9220 (pt) REVERT: Z 206 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9011 (mm-30) REVERT: Z 264 MET cc_start: 0.9292 (mmm) cc_final: 0.9042 (mmm) REVERT: Z 280 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8700 (tm-30) REVERT: Z 286 ILE cc_start: 0.9826 (tp) cc_final: 0.9559 (tp) REVERT: Z 290 ILE cc_start: 0.9610 (mm) cc_final: 0.9358 (mm) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2095 time to fit residues: 114.9608 Evaluate side-chains 300 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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: 0.5980 chunk 52 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 72 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.078628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.061639 restraints weight = 85176.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062895 restraints weight = 61129.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.063731 restraints weight = 47386.237| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13182 Z= 0.158 Angle : 0.661 10.598 17946 Z= 0.351 Chirality : 0.045 0.267 2226 Planarity : 0.005 0.065 2320 Dihedral : 3.910 16.195 1945 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 1.47 (0.19), residues: 1830 helix: 1.56 (0.13), residues: 1499 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 136 PHE 0.045 0.002 PHE L 62 TYR 0.030 0.002 TYR Z 277 ARG 0.012 0.001 ARG T 249 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 1284) hydrogen bonds : angle 3.91739 ( 3831) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.43904 ( 4) covalent geometry : bond 0.00350 (13180) covalent geometry : angle 0.66106 (17942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5020.60 seconds wall clock time: 87 minutes 8.74 seconds (5228.74 seconds total)