Starting phenix.real_space_refine on Thu Sep 18 01:14:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itw_60881/09_2025/9itw_60881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itw_60881/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9itw_60881/09_2025/9itw_60881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itw_60881/09_2025/9itw_60881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itw_60881/09_2025/9itw_60881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itw_60881/09_2025/9itw_60881.map" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} 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: {'TYR:plan': 2, 'ARG:plan': 19, 'ASN:plan1': 3, 'GLU:plan': 20, 'ASP:plan': 4, 'GLN:plan1': 11, 'HIS:plan': 1} 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: {'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 2} 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: {'ARG:plan': 1, 'PHE:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 3.27, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 465.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 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: 2.15 Time building geometry restraints manager: 1.28 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: 6.670 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.360 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG Y 138 TYR 0.023 0.001 TYR T 92 PHE 0.028 0.001 PHE T 222 TRP 0.008 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00446 (13180) covalent geometry : angle 0.68332 (17942) SS BOND : bond 0.74086 ( 2) SS BOND : angle 8.35350 ( 4) hydrogen bonds : bond 0.14716 ( 1284) hydrogen bonds : angle 5.13594 ( 3831) *********************** 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 : 0.482 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: 0.1014 time to fit residues: 77.5355 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 : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN M 43 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Z 253 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.079331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.063220 restraints weight = 84194.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.064483 restraints weight = 58489.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065198 restraints weight = 44963.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.065843 restraints weight = 37968.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.066322 restraints weight = 33074.328| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13182 Z= 0.163 Angle : 0.585 7.734 17946 Z= 0.315 Chirality : 0.041 0.236 2226 Planarity : 0.005 0.058 2320 Dihedral : 3.840 17.607 1945 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.18 % Allowed : 4.19 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG P 37 TYR 0.010 0.001 TYR L 48 PHE 0.033 0.002 PHE I 62 TRP 0.010 0.001 TRP T 208 HIS 0.003 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00335 (13180) covalent geometry : angle 0.58529 (17942) SS BOND : bond 0.01838 ( 2) SS BOND : angle 0.60296 ( 4) hydrogen bonds : bond 0.05101 ( 1284) hydrogen bonds : angle 4.05634 ( 3831) *********************** 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 421 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 419 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 33 VAL cc_start: 0.9537 (t) cc_final: 0.9266 (p) REVERT: Y 34 MET cc_start: 0.9080 (mmp) cc_final: 0.8560 (mmm) REVERT: Y 120 MET cc_start: 0.7491 (tpt) cc_final: 0.7221 (tpt) REVERT: V 34 MET cc_start: 0.8954 (tpt) cc_final: 0.8588 (tmm) REVERT: V 38 ASN cc_start: 0.9214 (m-40) cc_final: 0.8657 (m-40) REVERT: H 51 ILE cc_start: 0.9420 (mt) cc_final: 0.9195 (mt) REVERT: H 53 ILE cc_start: 0.9010 (tp) cc_final: 0.8591 (tp) REVERT: H 55 PHE cc_start: 0.9013 (m-80) cc_final: 0.8479 (m-80) REVERT: H 57 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8697 (pt0) REVERT: I 29 SER cc_start: 0.9232 (t) cc_final: 0.8991 (m) REVERT: I 48 TYR cc_start: 0.9055 (m-80) cc_final: 0.8203 (m-80) REVERT: I 49 MET cc_start: 0.9245 (ttp) cc_final: 0.8690 (tmm) REVERT: I 53 ILE cc_start: 0.8910 (mt) cc_final: 0.8656 (mt) REVERT: I 55 PHE cc_start: 0.8970 (m-10) cc_final: 0.8567 (m-10) REVERT: J 15 LEU cc_start: 0.9280 (mt) cc_final: 0.9016 (mp) REVERT: K 48 TYR cc_start: 0.9167 (m-10) cc_final: 0.8535 (m-80) REVERT: K 57 GLU cc_start: 0.9375 (tp30) cc_final: 0.8712 (pt0) REVERT: L 24 ILE cc_start: 0.9406 (mt) cc_final: 0.9080 (mm) REVERT: L 26 ILE cc_start: 0.9781 (mt) cc_final: 0.9526 (mt) REVERT: L 29 SER cc_start: 0.9620 (t) cc_final: 0.9317 (p) REVERT: L 33 GLN cc_start: 0.9442 (tt0) cc_final: 0.9160 (mm110) REVERT: L 48 TYR cc_start: 0.8856 (m-80) cc_final: 0.8012 (m-80) REVERT: L 57 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8331 (pt0) REVERT: L 62 PHE cc_start: 0.8680 (m-10) cc_final: 0.8355 (m-80) REVERT: N 43 ASN cc_start: 0.8794 (p0) cc_final: 0.8557 (p0) REVERT: N 51 ILE cc_start: 0.9365 (mt) cc_final: 0.9067 (tt) REVERT: N 55 PHE cc_start: 0.9376 (m-10) cc_final: 0.9088 (m-80) REVERT: N 57 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8005 (pt0) REVERT: N 59 LEU cc_start: 0.9374 (mm) cc_final: 0.9126 (mm) REVERT: N 62 PHE cc_start: 0.9356 (m-10) cc_final: 0.9042 (m-80) REVERT: N 66 ILE cc_start: 0.9349 (mm) cc_final: 0.9101 (mm) REVERT: O 11 LEU cc_start: 0.9550 (tt) cc_final: 0.9349 (tt) REVERT: O 57 GLU cc_start: 0.9452 (tp30) cc_final: 0.8930 (tp30) REVERT: O 59 LEU cc_start: 0.9540 (mt) cc_final: 0.9302 (mp) REVERT: O 62 PHE cc_start: 0.9376 (m-10) cc_final: 0.9160 (m-80) REVERT: P 20 PRO cc_start: 0.9345 (Cg_exo) cc_final: 0.9062 (Cg_endo) REVERT: P 24 ILE cc_start: 0.9490 (mt) cc_final: 0.9275 (mt) REVERT: P 33 GLN cc_start: 0.9559 (mt0) cc_final: 0.9081 (mm-40) REVERT: P 53 ILE cc_start: 0.9416 (pt) cc_final: 0.9117 (pt) REVERT: P 56 THR cc_start: 0.9118 (p) cc_final: 0.8568 (p) REVERT: P 57 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9166 (mm-30) REVERT: P 59 LEU cc_start: 0.9441 (mm) cc_final: 0.9110 (mm) REVERT: P 62 PHE cc_start: 0.9124 (m-10) cc_final: 0.8847 (m-80) REVERT: P 64 LEU cc_start: 0.9713 (mt) cc_final: 0.9430 (mt) REVERT: Q 1 MET cc_start: 0.6403 (mmm) cc_final: 0.6077 (mmm) REVERT: Q 68 PHE cc_start: 0.9078 (m-80) cc_final: 0.8736 (m-80) REVERT: T 244 PHE cc_start: 0.9118 (m-80) cc_final: 0.8709 (m-80) REVERT: T 264 MET cc_start: 0.9056 (mmt) cc_final: 0.8704 (tpp) REVERT: T 269 PRO cc_start: -0.4139 (Cg_endo) cc_final: -0.4402 (Cg_exo) REVERT: T 273 PRO cc_start: 0.5786 (Cg_exo) cc_final: 0.4942 (Cg_exo) REVERT: Z 89 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7955 (tm-30) REVERT: Z 125 LEU cc_start: 0.9192 (mp) cc_final: 0.8091 (mp) REVERT: Z 206 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8854 (mm-30) REVERT: Z 280 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8815 (tm-30) REVERT: Z 281 VAL cc_start: 0.9471 (p) cc_final: 0.8936 (p) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.0917 time to fit residues: 58.6641 Evaluate side-chains 344 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 111 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 50.0000 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.078847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.062030 restraints weight = 87813.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063332 restraints weight = 61157.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064061 restraints weight = 46665.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.064704 restraints weight = 39337.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.065126 restraints weight = 34198.199| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13182 Z= 0.171 Angle : 0.597 10.093 17946 Z= 0.323 Chirality : 0.041 0.197 2226 Planarity : 0.005 0.053 2320 Dihedral : 3.847 18.937 1945 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.27 % Allowed : 3.65 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.19), residues: 1830 helix: 1.63 (0.13), residues: 1479 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 73 TYR 0.015 0.001 TYR H 48 PHE 0.030 0.002 PHE T 236 TRP 0.010 0.001 TRP T 208 HIS 0.003 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00355 (13180) covalent geometry : angle 0.59661 (17942) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.17782 ( 4) hydrogen bonds : bond 0.04901 ( 1284) hydrogen bonds : angle 3.96586 ( 3831) *********************** 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 391 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 388 time to evaluate : 0.500 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: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9136 (mmp) cc_final: 0.8622 (mmm) REVERT: Y 90 GLN cc_start: 0.9022 (mp10) cc_final: 0.8816 (mp10) REVERT: Y 132 VAL cc_start: 0.9496 (p) cc_final: 0.9210 (m) REVERT: V 34 MET cc_start: 0.8933 (tpt) cc_final: 0.8705 (tmm) REVERT: V 89 GLN cc_start: 0.9418 (pt0) cc_final: 0.9156 (pp30) REVERT: H 50 PHE cc_start: 0.8883 (m-80) cc_final: 0.8621 (m-10) REVERT: H 51 ILE cc_start: 0.9460 (mt) cc_final: 0.9245 (mt) REVERT: H 53 ILE cc_start: 0.9079 (tp) cc_final: 0.8582 (tp) REVERT: H 55 PHE cc_start: 0.9035 (m-80) cc_final: 0.8587 (m-80) REVERT: H 57 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8544 (pt0) REVERT: I 48 TYR cc_start: 0.8988 (m-80) cc_final: 0.8189 (m-80) REVERT: I 49 MET cc_start: 0.9199 (ttp) cc_final: 0.8709 (tmm) REVERT: I 55 PHE cc_start: 0.8987 (m-10) cc_final: 0.8645 (m-80) REVERT: K 1 MET cc_start: 0.6466 (tpp) cc_final: 0.5846 (tpp) REVERT: K 48 TYR cc_start: 0.9156 (m-10) cc_final: 0.8538 (m-80) REVERT: K 49 MET cc_start: 0.9527 (ppp) cc_final: 0.9297 (ppp) REVERT: K 53 ILE cc_start: 0.9467 (mm) cc_final: 0.9196 (mm) REVERT: K 57 GLU cc_start: 0.9362 (tp30) cc_final: 0.8838 (pt0) REVERT: L 24 ILE cc_start: 0.9411 (mt) cc_final: 0.9130 (mm) REVERT: L 26 ILE cc_start: 0.9765 (mt) cc_final: 0.9475 (tt) REVERT: L 29 SER cc_start: 0.9615 (t) cc_final: 0.9268 (p) REVERT: L 33 GLN cc_start: 0.9451 (tt0) cc_final: 0.9114 (mm110) REVERT: L 48 TYR cc_start: 0.8907 (m-80) cc_final: 0.7832 (m-80) REVERT: L 57 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8311 (pt0) REVERT: L 62 PHE cc_start: 0.8730 (m-10) cc_final: 0.8473 (m-80) REVERT: M 41 ILE cc_start: 0.8735 (tp) cc_final: 0.8261 (tt) REVERT: N 43 ASN cc_start: 0.8951 (p0) cc_final: 0.8667 (p0) REVERT: N 51 ILE cc_start: 0.9454 (mt) cc_final: 0.9076 (tt) REVERT: N 55 PHE cc_start: 0.9379 (m-10) cc_final: 0.9097 (m-80) REVERT: N 64 LEU cc_start: 0.9358 (mt) cc_final: 0.8988 (mt) REVERT: N 66 ILE cc_start: 0.9349 (mm) cc_final: 0.9072 (mm) REVERT: O 57 GLU cc_start: 0.9435 (tp30) cc_final: 0.8891 (tp30) REVERT: O 59 LEU cc_start: 0.9570 (mt) cc_final: 0.9304 (mp) REVERT: O 62 PHE cc_start: 0.9368 (m-10) cc_final: 0.9167 (m-80) REVERT: P 20 PRO cc_start: 0.9326 (Cg_exo) cc_final: 0.9112 (Cg_endo) REVERT: P 33 GLN cc_start: 0.9568 (mt0) cc_final: 0.9054 (mm-40) REVERT: P 53 ILE cc_start: 0.9448 (pt) cc_final: 0.9170 (pt) REVERT: P 57 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9189 (mm-30) REVERT: P 59 LEU cc_start: 0.9469 (mm) cc_final: 0.9143 (mm) REVERT: Q 1 MET cc_start: 0.6632 (mmm) cc_final: 0.6114 (mmm) REVERT: Q 18 ILE cc_start: 0.9003 (mt) cc_final: 0.8771 (mt) REVERT: Q 50 PHE cc_start: 0.9368 (m-80) cc_final: 0.8994 (m-80) REVERT: Q 55 PHE cc_start: 0.9101 (m-10) cc_final: 0.8826 (m-80) REVERT: Q 68 PHE cc_start: 0.9020 (m-80) cc_final: 0.8695 (m-80) REVERT: T 244 PHE cc_start: 0.9122 (m-80) cc_final: 0.8815 (m-80) REVERT: T 264 MET cc_start: 0.9035 (mmt) cc_final: 0.8589 (tpp) REVERT: T 273 PRO cc_start: 0.6034 (Cg_exo) cc_final: 0.5135 (Cg_exo) REVERT: Z 89 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7957 (tm-30) REVERT: Z 125 LEU cc_start: 0.9143 (mp) cc_final: 0.7756 (mp) REVERT: Z 206 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8888 (mm-30) REVERT: Z 280 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8729 (tm-30) REVERT: Z 281 VAL cc_start: 0.9451 (p) cc_final: 0.8886 (p) outliers start: 3 outliers final: 1 residues processed: 391 average time/residue: 0.0959 time to fit residues: 57.2450 Evaluate side-chains 329 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 115 GLN V 149 HIS ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.079759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062897 restraints weight = 88474.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064269 restraints weight = 60988.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.065184 restraints weight = 46216.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065515 restraints weight = 37998.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.066028 restraints weight = 34167.531| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13182 Z= 0.154 Angle : 0.601 7.661 17946 Z= 0.321 Chirality : 0.043 0.474 2226 Planarity : 0.005 0.058 2320 Dihedral : 3.870 18.153 1945 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.19), residues: 1830 helix: 1.52 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 99 TYR 0.013 0.001 TYR H 48 PHE 0.038 0.001 PHE I 62 TRP 0.009 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00327 (13180) covalent geometry : angle 0.60082 (17942) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.41538 ( 4) hydrogen bonds : bond 0.04628 ( 1284) hydrogen bonds : angle 3.89723 ( 3831) *********************** 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 388 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 0.496 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: 0.9152 (mmp) cc_final: 0.8722 (mmm) REVERT: Y 117 ARG cc_start: 0.9378 (tmm-80) cc_final: 0.9080 (ttp-110) REVERT: V 34 MET cc_start: 0.8981 (tpt) cc_final: 0.8714 (tmm) REVERT: V 149 HIS cc_start: 0.8870 (p90) cc_final: 0.8630 (p-80) REVERT: H 50 PHE cc_start: 0.8909 (m-80) cc_final: 0.8611 (m-10) REVERT: H 51 ILE cc_start: 0.9444 (mt) cc_final: 0.9167 (mt) REVERT: H 53 ILE cc_start: 0.9041 (tp) cc_final: 0.8554 (tp) REVERT: H 57 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8366 (pt0) REVERT: I 29 SER cc_start: 0.9280 (t) cc_final: 0.9045 (p) REVERT: I 48 TYR cc_start: 0.9070 (m-80) cc_final: 0.8200 (m-80) REVERT: I 49 MET cc_start: 0.9210 (ttp) cc_final: 0.8765 (tmm) REVERT: I 57 GLU cc_start: 0.8616 (tp30) cc_final: 0.8350 (mt-10) REVERT: K 20 PRO cc_start: 0.9387 (Cg_exo) cc_final: 0.9163 (Cg_endo) REVERT: K 53 ILE cc_start: 0.9460 (mm) cc_final: 0.8901 (tp) REVERT: K 57 GLU cc_start: 0.9328 (tp30) cc_final: 0.8763 (pt0) REVERT: L 1 MET cc_start: 0.7609 (tpt) cc_final: 0.7394 (tmm) REVERT: L 24 ILE cc_start: 0.9370 (mt) cc_final: 0.9039 (mm) REVERT: L 26 ILE cc_start: 0.9768 (mt) cc_final: 0.9446 (tt) REVERT: L 29 SER cc_start: 0.9606 (t) cc_final: 0.9274 (p) REVERT: L 33 GLN cc_start: 0.9436 (tt0) cc_final: 0.9080 (mm110) REVERT: L 48 TYR cc_start: 0.8846 (m-80) cc_final: 0.7846 (m-80) REVERT: L 57 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8153 (pt0) REVERT: L 62 PHE cc_start: 0.8742 (m-10) cc_final: 0.8431 (m-80) REVERT: M 1 MET cc_start: 0.7374 (mmp) cc_final: 0.6978 (mmm) REVERT: M 41 ILE cc_start: 0.8721 (tp) cc_final: 0.8261 (tt) REVERT: M 56 THR cc_start: 0.9306 (t) cc_final: 0.9101 (p) REVERT: N 1 MET cc_start: 0.6603 (mtt) cc_final: 0.6058 (mtp) REVERT: N 43 ASN cc_start: 0.8965 (p0) cc_final: 0.8678 (p0) REVERT: N 51 ILE cc_start: 0.9447 (mt) cc_final: 0.9057 (tt) REVERT: N 55 PHE cc_start: 0.9374 (m-10) cc_final: 0.9111 (m-80) REVERT: N 57 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8236 (mt-10) REVERT: N 62 PHE cc_start: 0.9358 (m-10) cc_final: 0.9013 (m-80) REVERT: N 66 ILE cc_start: 0.9333 (mm) cc_final: 0.9092 (mm) REVERT: O 57 GLU cc_start: 0.9430 (tp30) cc_final: 0.8848 (tp30) REVERT: O 59 LEU cc_start: 0.9591 (mt) cc_final: 0.9338 (mp) REVERT: P 20 PRO cc_start: 0.9325 (Cg_exo) cc_final: 0.8980 (Cg_endo) REVERT: P 33 GLN cc_start: 0.9578 (mt0) cc_final: 0.9131 (mm-40) REVERT: P 56 THR cc_start: 0.9231 (p) cc_final: 0.8721 (t) REVERT: P 57 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9185 (mm-30) REVERT: P 64 LEU cc_start: 0.9724 (mt) cc_final: 0.9354 (mt) REVERT: P 68 PHE cc_start: 0.9113 (m-80) cc_final: 0.8474 (m-80) REVERT: Q 1 MET cc_start: 0.6594 (mmm) cc_final: 0.5996 (mmm) REVERT: Q 18 ILE cc_start: 0.8892 (mt) cc_final: 0.8646 (mt) REVERT: Q 50 PHE cc_start: 0.9405 (m-80) cc_final: 0.9149 (m-80) REVERT: Q 53 ILE cc_start: 0.8579 (mt) cc_final: 0.8260 (mt) REVERT: Q 55 PHE cc_start: 0.9087 (m-10) cc_final: 0.8751 (m-80) REVERT: Q 57 GLU cc_start: 0.9125 (pm20) cc_final: 0.8695 (pm20) REVERT: Q 68 PHE cc_start: 0.9042 (m-80) cc_final: 0.8685 (m-80) REVERT: T 264 MET cc_start: 0.9035 (mmt) cc_final: 0.8690 (tpp) REVERT: Z 125 LEU cc_start: 0.9126 (mp) cc_final: 0.7698 (mp) REVERT: Z 206 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8960 (mm-30) REVERT: Z 280 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8684 (tm-30) REVERT: Z 281 VAL cc_start: 0.9482 (p) cc_final: 0.8933 (p) outliers start: 2 outliers final: 2 residues processed: 388 average time/residue: 0.0964 time to fit residues: 57.3227 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 126 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 33 GLN ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063032 restraints weight = 90454.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064388 restraints weight = 62310.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.065250 restraints weight = 47470.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.065931 restraints weight = 39211.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.066384 restraints weight = 33890.198| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13182 Z= 0.150 Angle : 0.597 8.232 17946 Z= 0.320 Chirality : 0.042 0.400 2226 Planarity : 0.005 0.058 2320 Dihedral : 3.812 16.827 1945 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.19), residues: 1830 helix: 1.51 (0.13), residues: 1475 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 37 TYR 0.028 0.001 TYR Z 277 PHE 0.043 0.002 PHE Q 62 TRP 0.009 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 136 Details of bonding type rmsd covalent geometry : bond 0.00323 (13180) covalent geometry : angle 0.59730 (17942) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.43511 ( 4) hydrogen bonds : bond 0.04539 ( 1284) hydrogen bonds : angle 3.82824 ( 3831) *********************** 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 378 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9136 (mmp) cc_final: 0.8716 (mmm) REVERT: Y 90 GLN cc_start: 0.9063 (mp10) cc_final: 0.8725 (mp10) REVERT: Y 120 MET cc_start: 0.7197 (tpt) cc_final: 0.6558 (ttt) REVERT: H 50 PHE cc_start: 0.8867 (m-80) cc_final: 0.8612 (m-10) REVERT: H 53 ILE cc_start: 0.9015 (tp) cc_final: 0.8438 (tp) REVERT: H 55 PHE cc_start: 0.9010 (m-80) cc_final: 0.8767 (m-80) REVERT: H 57 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8573 (pt0) REVERT: I 1 MET cc_start: 0.7989 (mtp) cc_final: 0.7420 (ttt) REVERT: I 29 SER cc_start: 0.9282 (t) cc_final: 0.9031 (p) REVERT: I 48 TYR cc_start: 0.9106 (m-80) cc_final: 0.8290 (m-80) REVERT: I 49 MET cc_start: 0.9211 (ttp) cc_final: 0.8805 (tmm) REVERT: I 57 GLU cc_start: 0.8499 (tp30) cc_final: 0.8269 (mt-10) REVERT: K 20 PRO cc_start: 0.9415 (Cg_exo) cc_final: 0.9195 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9403 (m-80) cc_final: 0.8812 (m-80) REVERT: K 53 ILE cc_start: 0.9540 (mm) cc_final: 0.8766 (tp) REVERT: K 57 GLU cc_start: 0.9312 (tp30) cc_final: 0.8735 (pt0) REVERT: L 15 LEU cc_start: 0.9128 (mp) cc_final: 0.8927 (mp) REVERT: L 24 ILE cc_start: 0.9376 (mt) cc_final: 0.9078 (mm) REVERT: L 26 ILE cc_start: 0.9767 (mt) cc_final: 0.9439 (tt) REVERT: L 29 SER cc_start: 0.9574 (t) cc_final: 0.9258 (p) REVERT: L 33 GLN cc_start: 0.9449 (tt0) cc_final: 0.9064 (mm110) REVERT: L 48 TYR cc_start: 0.8834 (m-80) cc_final: 0.7831 (m-80) REVERT: L 53 ILE cc_start: 0.9375 (tp) cc_final: 0.9090 (tt) REVERT: L 57 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8153 (pt0) REVERT: L 62 PHE cc_start: 0.8748 (m-10) cc_final: 0.8466 (m-80) REVERT: M 41 ILE cc_start: 0.8759 (tp) cc_final: 0.8318 (tt) REVERT: N 43 ASN cc_start: 0.8963 (p0) cc_final: 0.8682 (p0) REVERT: N 51 ILE cc_start: 0.9389 (mt) cc_final: 0.8818 (tt) REVERT: N 55 PHE cc_start: 0.9323 (m-10) cc_final: 0.8919 (m-80) REVERT: N 57 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8108 (mt-10) REVERT: N 62 PHE cc_start: 0.9322 (m-10) cc_final: 0.9061 (m-80) REVERT: N 66 ILE cc_start: 0.9328 (mm) cc_final: 0.9078 (mm) REVERT: O 50 PHE cc_start: 0.9094 (m-10) cc_final: 0.8864 (m-80) REVERT: O 57 GLU cc_start: 0.9456 (tp30) cc_final: 0.8817 (tp30) REVERT: O 62 PHE cc_start: 0.9168 (m-80) cc_final: 0.8902 (m-80) REVERT: P 20 PRO cc_start: 0.9330 (Cg_exo) cc_final: 0.9010 (Cg_endo) REVERT: P 27 ILE cc_start: 0.9415 (mt) cc_final: 0.9139 (mt) REVERT: P 56 THR cc_start: 0.9173 (p) cc_final: 0.8692 (t) REVERT: P 57 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9185 (mm-30) REVERT: P 62 PHE cc_start: 0.9265 (m-80) cc_final: 0.8920 (m-80) REVERT: P 64 LEU cc_start: 0.9675 (mt) cc_final: 0.9356 (mt) REVERT: P 68 PHE cc_start: 0.9209 (m-80) cc_final: 0.8573 (m-80) REVERT: Q 1 MET cc_start: 0.6444 (mmm) cc_final: 0.5825 (mmm) REVERT: Q 18 ILE cc_start: 0.8791 (mt) cc_final: 0.8526 (mt) REVERT: Q 50 PHE cc_start: 0.9395 (m-80) cc_final: 0.9194 (m-80) REVERT: Q 53 ILE cc_start: 0.8567 (mt) cc_final: 0.8207 (mt) REVERT: Q 68 PHE cc_start: 0.9068 (m-80) cc_final: 0.8688 (m-80) REVERT: T 264 MET cc_start: 0.9028 (mmt) cc_final: 0.8699 (tpp) REVERT: T 286 ILE cc_start: 0.9503 (pt) cc_final: 0.9294 (pt) REVERT: Z 84 MET cc_start: 0.9205 (tpp) cc_final: 0.8705 (tmm) REVERT: Z 206 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8964 (mm-30) REVERT: Z 280 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8666 (tp30) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.0947 time to fit residues: 54.7830 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 : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 170 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 HIS ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.079729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.063064 restraints weight = 90037.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.064361 restraints weight = 62269.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.065186 restraints weight = 47684.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.065827 restraints weight = 39606.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066285 restraints weight = 34326.695| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13182 Z= 0.147 Angle : 0.602 8.715 17946 Z= 0.321 Chirality : 0.042 0.363 2226 Planarity : 0.005 0.059 2320 Dihedral : 3.827 15.886 1945 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1830 helix: 1.48 (0.13), residues: 1473 sheet: None (None), residues: 0 loop : -1.52 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 62 TYR 0.021 0.001 TYR Z 277 PHE 0.051 0.002 PHE T 236 TRP 0.009 0.001 TRP T 208 HIS 0.003 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00314 (13180) covalent geometry : angle 0.60245 (17942) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.42565 ( 4) hydrogen bonds : bond 0.04448 ( 1284) hydrogen bonds : angle 3.83904 ( 3831) *********************** 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 376 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.515 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: 0.9052 (mmp) cc_final: 0.8694 (mmm) REVERT: Y 117 ARG cc_start: 0.9341 (tmm-80) cc_final: 0.8967 (ttm110) REVERT: Y 120 MET cc_start: 0.7378 (tpt) cc_final: 0.6787 (ttt) REVERT: V 21 LEU cc_start: 0.9502 (tp) cc_final: 0.9215 (tt) REVERT: V 25 LEU cc_start: 0.9616 (mt) cc_final: 0.9366 (mt) REVERT: V 34 MET cc_start: 0.8867 (mmm) cc_final: 0.8480 (tpp) REVERT: V 82 GLN cc_start: 0.9322 (tp-100) cc_final: 0.9122 (tp-100) REVERT: H 29 SER cc_start: 0.9379 (t) cc_final: 0.9121 (m) REVERT: H 50 PHE cc_start: 0.8863 (m-80) cc_final: 0.8614 (m-10) REVERT: H 53 ILE cc_start: 0.9100 (tp) cc_final: 0.8593 (tp) REVERT: H 55 PHE cc_start: 0.9017 (m-80) cc_final: 0.8631 (m-80) REVERT: H 57 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8456 (pt0) REVERT: I 1 MET cc_start: 0.8019 (mtp) cc_final: 0.7540 (ttt) REVERT: I 29 SER cc_start: 0.9326 (t) cc_final: 0.9064 (p) REVERT: I 48 TYR cc_start: 0.9079 (m-80) cc_final: 0.8262 (m-80) REVERT: I 49 MET cc_start: 0.9239 (ttp) cc_final: 0.8884 (tmm) REVERT: I 57 GLU cc_start: 0.8494 (tp30) cc_final: 0.8262 (pt0) REVERT: K 20 PRO cc_start: 0.9441 (Cg_exo) cc_final: 0.9208 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9356 (m-80) cc_final: 0.8915 (m-80) REVERT: K 53 ILE cc_start: 0.9579 (mm) cc_final: 0.9203 (mm) REVERT: K 57 GLU cc_start: 0.9237 (tp30) cc_final: 0.8706 (pt0) REVERT: L 26 ILE cc_start: 0.9770 (mt) cc_final: 0.9468 (tt) REVERT: L 29 SER cc_start: 0.9587 (t) cc_final: 0.9281 (p) REVERT: L 33 GLN cc_start: 0.9438 (tt0) cc_final: 0.9102 (mm110) REVERT: L 48 TYR cc_start: 0.8814 (m-80) cc_final: 0.7818 (m-80) REVERT: L 56 THR cc_start: 0.9248 (t) cc_final: 0.9040 (t) REVERT: L 62 PHE cc_start: 0.8676 (m-10) cc_final: 0.8430 (m-80) REVERT: M 41 ILE cc_start: 0.8757 (tp) cc_final: 0.8263 (tt) REVERT: N 43 ASN cc_start: 0.8953 (p0) cc_final: 0.8662 (p0) REVERT: N 51 ILE cc_start: 0.9330 (mt) cc_final: 0.8732 (tt) REVERT: N 55 PHE cc_start: 0.9270 (m-10) cc_final: 0.8865 (m-80) REVERT: N 62 PHE cc_start: 0.9254 (m-10) cc_final: 0.8998 (m-80) REVERT: N 66 ILE cc_start: 0.9337 (mm) cc_final: 0.9117 (mm) REVERT: O 50 PHE cc_start: 0.9109 (m-10) cc_final: 0.8751 (m-80) REVERT: O 57 GLU cc_start: 0.9419 (tp30) cc_final: 0.8849 (tp30) REVERT: O 62 PHE cc_start: 0.9168 (m-80) cc_final: 0.8890 (m-80) REVERT: P 20 PRO cc_start: 0.9317 (Cg_exo) cc_final: 0.9033 (Cg_endo) REVERT: P 56 THR cc_start: 0.9092 (p) cc_final: 0.8571 (t) REVERT: P 57 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9171 (mm-30) REVERT: P 59 LEU cc_start: 0.9509 (mm) cc_final: 0.9281 (mm) REVERT: P 62 PHE cc_start: 0.9238 (m-80) cc_final: 0.8883 (m-80) REVERT: P 64 LEU cc_start: 0.9644 (mt) cc_final: 0.9402 (mt) REVERT: Q 1 MET cc_start: 0.6479 (mmm) cc_final: 0.5842 (mmm) REVERT: Q 50 PHE cc_start: 0.9409 (m-80) cc_final: 0.9123 (m-80) REVERT: Q 68 PHE cc_start: 0.8941 (m-80) cc_final: 0.8630 (m-80) REVERT: T 264 MET cc_start: 0.9008 (mmt) cc_final: 0.8781 (tpp) REVERT: Z 84 MET cc_start: 0.9134 (tpp) cc_final: 0.8679 (tmm) REVERT: Z 125 LEU cc_start: 0.9234 (mp) cc_final: 0.8800 (mm) REVERT: Z 206 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8935 (mm-30) REVERT: Z 235 GLU cc_start: 0.8517 (pt0) cc_final: 0.8313 (pt0) REVERT: Z 280 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8614 (tm-30) outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.0956 time to fit residues: 55.3359 Evaluate side-chains 317 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 147 optimal weight: 0.0470 chunk 166 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 HIS T 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.079457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.062960 restraints weight = 90091.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064301 restraints weight = 62592.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.065109 restraints weight = 47776.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.065786 restraints weight = 39679.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066238 restraints weight = 34241.995| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13182 Z= 0.154 Angle : 0.602 9.316 17946 Z= 0.325 Chirality : 0.042 0.344 2226 Planarity : 0.005 0.061 2320 Dihedral : 3.786 18.722 1945 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.09 % Allowed : 1.55 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 1830 helix: 1.53 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.56 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 37 TYR 0.018 0.001 TYR Z 277 PHE 0.033 0.002 PHE Q 62 TRP 0.009 0.001 TRP T 208 HIS 0.002 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00333 (13180) covalent geometry : angle 0.60211 (17942) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.43490 ( 4) hydrogen bonds : bond 0.04472 ( 1284) hydrogen bonds : angle 3.84362 ( 3831) *********************** 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 365 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.479 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: 0.9112 (mmp) cc_final: 0.8758 (mmm) REVERT: Y 90 GLN cc_start: 0.9067 (mp10) cc_final: 0.8775 (mp10) REVERT: V 21 LEU cc_start: 0.9533 (tp) cc_final: 0.9262 (tt) REVERT: V 25 LEU cc_start: 0.9654 (mt) cc_final: 0.9392 (mt) REVERT: H 29 SER cc_start: 0.9369 (t) cc_final: 0.9108 (m) REVERT: H 50 PHE cc_start: 0.8834 (m-80) cc_final: 0.8598 (m-10) REVERT: H 55 PHE cc_start: 0.9159 (m-80) cc_final: 0.8808 (m-80) REVERT: H 57 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8632 (mt-10) REVERT: H 62 PHE cc_start: 0.9102 (m-10) cc_final: 0.8755 (m-80) REVERT: I 1 MET cc_start: 0.8261 (mtp) cc_final: 0.7740 (ttt) REVERT: I 29 SER cc_start: 0.9311 (t) cc_final: 0.9036 (p) REVERT: I 49 MET cc_start: 0.9247 (ttp) cc_final: 0.8969 (tmm) REVERT: I 57 GLU cc_start: 0.8592 (tp30) cc_final: 0.8333 (mt-10) REVERT: J 1 MET cc_start: 0.7529 (mmt) cc_final: 0.7290 (mpp) REVERT: J 28 VAL cc_start: 0.9510 (t) cc_final: 0.9257 (m) REVERT: K 20 PRO cc_start: 0.9444 (Cg_exo) cc_final: 0.9237 (Cg_endo) REVERT: K 48 TYR cc_start: 0.9429 (m-80) cc_final: 0.8784 (m-80) REVERT: K 53 ILE cc_start: 0.9565 (mm) cc_final: 0.8729 (tp) REVERT: K 57 GLU cc_start: 0.9246 (tp30) cc_final: 0.8638 (pt0) REVERT: L 26 ILE cc_start: 0.9746 (mt) cc_final: 0.9433 (tt) REVERT: L 29 SER cc_start: 0.9552 (t) cc_final: 0.9268 (p) REVERT: L 33 GLN cc_start: 0.9469 (tt0) cc_final: 0.9104 (mm110) REVERT: L 48 TYR cc_start: 0.8833 (m-80) cc_final: 0.7823 (m-80) REVERT: L 62 PHE cc_start: 0.8729 (m-10) cc_final: 0.8464 (m-80) REVERT: M 41 ILE cc_start: 0.8834 (tp) cc_final: 0.8330 (tt) REVERT: N 43 ASN cc_start: 0.8976 (p0) cc_final: 0.8692 (p0) REVERT: N 51 ILE cc_start: 0.9355 (mt) cc_final: 0.8734 (tt) REVERT: N 55 PHE cc_start: 0.9283 (m-10) cc_final: 0.8868 (m-80) REVERT: N 62 PHE cc_start: 0.9300 (m-10) cc_final: 0.9046 (m-80) REVERT: N 66 ILE cc_start: 0.9333 (mm) cc_final: 0.9104 (mm) REVERT: O 40 GLU cc_start: 0.9343 (mp0) cc_final: 0.9110 (pp20) REVERT: O 50 PHE cc_start: 0.9118 (m-10) cc_final: 0.8807 (m-80) REVERT: O 57 GLU cc_start: 0.9551 (tp30) cc_final: 0.8813 (tp30) REVERT: P 27 ILE cc_start: 0.9159 (mt) cc_final: 0.8924 (mt) REVERT: P 55 PHE cc_start: 0.9089 (m-80) cc_final: 0.8336 (m-80) REVERT: P 57 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9211 (mm-30) REVERT: P 59 LEU cc_start: 0.9498 (mm) cc_final: 0.9231 (mm) REVERT: P 62 PHE cc_start: 0.9260 (m-80) cc_final: 0.8912 (m-80) REVERT: P 68 PHE cc_start: 0.9310 (m-80) cc_final: 0.9101 (m-80) REVERT: Q 1 MET cc_start: 0.6466 (mmm) cc_final: 0.5829 (mmm) REVERT: Q 18 ILE cc_start: 0.8584 (mt) cc_final: 0.8351 (mt) REVERT: Q 57 GLU cc_start: 0.9074 (pm20) cc_final: 0.8581 (pm20) REVERT: Q 68 PHE cc_start: 0.9033 (m-80) cc_final: 0.8664 (m-80) REVERT: T 244 PHE cc_start: 0.9088 (m-80) cc_final: 0.8793 (m-80) REVERT: T 264 MET cc_start: 0.8993 (mmt) cc_final: 0.8751 (tpp) REVERT: T 282 PHE cc_start: 0.9047 (t80) cc_final: 0.8748 (t80) REVERT: T 286 ILE cc_start: 0.9492 (pt) cc_final: 0.9266 (pt) REVERT: Z 84 MET cc_start: 0.9211 (tpp) cc_final: 0.8811 (tmm) REVERT: Z 125 LEU cc_start: 0.9242 (mp) cc_final: 0.8921 (mm) REVERT: Z 206 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9007 (mm-30) REVERT: Z 235 GLU cc_start: 0.8534 (pt0) cc_final: 0.8311 (pt0) REVERT: Z 280 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8691 (tm-30) outliers start: 1 outliers final: 1 residues processed: 365 average time/residue: 0.0941 time to fit residues: 52.9149 Evaluate side-chains 308 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 102 optimal weight: 0.1980 chunk 148 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 HIS 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 = 0.078514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061462 restraints weight = 87746.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.062647 restraints weight = 61968.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.063536 restraints weight = 48940.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064101 restraints weight = 40617.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.064512 restraints weight = 35471.939| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4703 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= 0.176 Angle : 0.632 9.638 17946 Z= 0.340 Chirality : 0.044 0.485 2226 Planarity : 0.005 0.066 2320 Dihedral : 3.808 17.027 1945 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 1830 helix: 1.48 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -1.57 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 119 TYR 0.018 0.002 TYR Z 277 PHE 0.035 0.002 PHE I 62 TRP 0.012 0.001 TRP T 208 HIS 0.003 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00380 (13180) covalent geometry : angle 0.63245 (17942) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.43512 ( 4) hydrogen bonds : bond 0.04525 ( 1284) hydrogen bonds : angle 3.89858 ( 3831) *********************** 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 360 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.478 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: 0.9140 (mmp) cc_final: 0.8787 (mmm) REVERT: Y 117 ARG cc_start: 0.9340 (tmm-80) cc_final: 0.9097 (ttp-110) REVERT: V 25 LEU cc_start: 0.9662 (mt) cc_final: 0.9445 (mt) REVERT: V 82 GLN cc_start: 0.9460 (tp-100) cc_final: 0.9239 (tp-100) REVERT: X 18 PHE cc_start: 0.3616 (t80) cc_final: 0.3281 (m-10) REVERT: X 21 LEU cc_start: 0.7849 (pp) cc_final: 0.7556 (pp) REVERT: H 50 PHE cc_start: 0.8843 (m-80) cc_final: 0.8638 (m-10) REVERT: H 53 ILE cc_start: 0.9150 (tp) cc_final: 0.8650 (tp) REVERT: H 55 PHE cc_start: 0.9177 (m-80) cc_final: 0.8704 (m-80) REVERT: H 57 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8680 (mt-10) REVERT: H 62 PHE cc_start: 0.9130 (m-10) cc_final: 0.8747 (m-80) REVERT: I 1 MET cc_start: 0.8217 (mtp) cc_final: 0.7682 (ttt) REVERT: I 29 SER cc_start: 0.9316 (t) cc_final: 0.9057 (p) REVERT: I 48 TYR cc_start: 0.9244 (m-80) cc_final: 0.8488 (m-80) REVERT: I 49 MET cc_start: 0.9263 (ttp) cc_final: 0.8855 (tmm) REVERT: I 57 GLU cc_start: 0.8680 (tp30) cc_final: 0.8404 (pt0) REVERT: J 1 MET cc_start: 0.7401 (mmt) cc_final: 0.7153 (mpp) REVERT: J 28 VAL cc_start: 0.9503 (t) cc_final: 0.9259 (m) REVERT: J 55 PHE cc_start: 0.9194 (m-80) cc_final: 0.8985 (m-80) REVERT: K 11 LEU cc_start: 0.9595 (tt) cc_final: 0.9389 (tt) REVERT: K 20 PRO cc_start: 0.9459 (Cg_exo) cc_final: 0.9244 (Cg_endo) REVERT: K 45 VAL cc_start: 0.9660 (t) cc_final: 0.9384 (t) REVERT: K 48 TYR cc_start: 0.9441 (m-80) cc_final: 0.8819 (m-80) REVERT: K 53 ILE cc_start: 0.9365 (mm) cc_final: 0.8798 (tp) REVERT: K 57 GLU cc_start: 0.9258 (tp30) cc_final: 0.8668 (pt0) REVERT: L 26 ILE cc_start: 0.9768 (mt) cc_final: 0.9483 (tt) REVERT: L 29 SER cc_start: 0.9572 (t) cc_final: 0.9263 (p) REVERT: L 33 GLN cc_start: 0.9476 (tt0) cc_final: 0.9121 (mm110) REVERT: L 48 TYR cc_start: 0.8854 (m-80) cc_final: 0.8070 (m-80) REVERT: L 62 PHE cc_start: 0.8681 (m-10) cc_final: 0.8457 (m-80) REVERT: M 41 ILE cc_start: 0.8879 (tp) cc_final: 0.8429 (tt) REVERT: N 43 ASN cc_start: 0.8984 (p0) cc_final: 0.8713 (p0) REVERT: N 51 ILE cc_start: 0.9350 (mt) cc_final: 0.8759 (tt) REVERT: N 55 PHE cc_start: 0.9279 (m-10) cc_final: 0.8868 (m-80) REVERT: N 66 ILE cc_start: 0.9359 (mm) cc_final: 0.9137 (mm) REVERT: O 40 GLU cc_start: 0.9354 (mp0) cc_final: 0.9140 (pp20) REVERT: O 50 PHE cc_start: 0.9052 (m-10) cc_final: 0.8840 (m-80) REVERT: O 57 GLU cc_start: 0.9544 (tp30) cc_final: 0.8908 (tp30) REVERT: O 62 PHE cc_start: 0.9139 (m-80) cc_final: 0.8926 (m-80) REVERT: P 27 ILE cc_start: 0.9181 (mt) cc_final: 0.8954 (mt) REVERT: P 55 PHE cc_start: 0.9125 (m-80) cc_final: 0.8471 (m-10) REVERT: P 57 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9234 (mm-30) REVERT: P 59 LEU cc_start: 0.9496 (mm) cc_final: 0.9230 (mm) REVERT: P 62 PHE cc_start: 0.9223 (m-80) cc_final: 0.8904 (m-80) REVERT: P 68 PHE cc_start: 0.9299 (m-80) cc_final: 0.9092 (m-80) REVERT: Q 1 MET cc_start: 0.6294 (mmm) cc_final: 0.5675 (mmm) REVERT: Q 18 ILE cc_start: 0.8772 (mt) cc_final: 0.8530 (mt) REVERT: Q 50 PHE cc_start: 0.9416 (m-80) cc_final: 0.9158 (m-80) REVERT: Q 55 PHE cc_start: 0.8891 (m-80) cc_final: 0.8373 (m-80) REVERT: Q 68 PHE cc_start: 0.9060 (m-80) cc_final: 0.8663 (m-80) REVERT: T 244 PHE cc_start: 0.9064 (m-80) cc_final: 0.8769 (m-80) REVERT: T 264 MET cc_start: 0.8999 (mmt) cc_final: 0.8751 (tpp) REVERT: T 282 PHE cc_start: 0.9051 (t80) cc_final: 0.8848 (t80) REVERT: T 286 ILE cc_start: 0.9519 (pt) cc_final: 0.9301 (pt) REVERT: Z 206 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9002 (mm-30) REVERT: Z 235 GLU cc_start: 0.8489 (pt0) cc_final: 0.8286 (pt0) REVERT: Z 280 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8699 (tm-30) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.0948 time to fit residues: 52.3628 Evaluate side-chains 307 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 115 GLN V 90 GLN V 149 HIS T 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.079284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.062460 restraints weight = 89474.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.063748 restraints weight = 62051.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.064588 restraints weight = 47659.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.065249 restraints weight = 39588.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.065705 restraints weight = 34324.594| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13182 Z= 0.152 Angle : 0.654 10.216 17946 Z= 0.343 Chirality : 0.045 0.473 2226 Planarity : 0.005 0.064 2320 Dihedral : 3.916 22.374 1945 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.19), residues: 1830 helix: 1.55 (0.13), residues: 1503 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Y 119 TYR 0.016 0.001 TYR Z 277 PHE 0.033 0.002 PHE O 62 TRP 0.008 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 136 Details of bonding type rmsd covalent geometry : bond 0.00337 (13180) covalent geometry : angle 0.65394 (17942) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.42933 ( 4) hydrogen bonds : bond 0.04499 ( 1284) hydrogen bonds : angle 3.87475 ( 3831) *********************** 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 367 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9072 (mmp) cc_final: 0.8737 (mmm) REVERT: Y 90 GLN cc_start: 0.9010 (mp10) cc_final: 0.8727 (mp10) REVERT: Y 117 ARG cc_start: 0.9379 (tmm-80) cc_final: 0.9003 (ttm110) REVERT: Y 120 MET cc_start: 0.7332 (tpt) cc_final: 0.6689 (ttt) REVERT: H 29 SER cc_start: 0.9352 (t) cc_final: 0.9097 (m) REVERT: H 49 MET cc_start: 0.9122 (ppp) cc_final: 0.8580 (ppp) REVERT: H 50 PHE cc_start: 0.8893 (m-80) cc_final: 0.8580 (m-10) REVERT: H 53 ILE cc_start: 0.9156 (tp) cc_final: 0.8754 (tp) REVERT: H 62 PHE cc_start: 0.9122 (m-10) cc_final: 0.8743 (m-80) REVERT: I 1 MET cc_start: 0.8194 (mtp) cc_final: 0.7700 (ttt) REVERT: I 29 SER cc_start: 0.9323 (t) cc_final: 0.9039 (p) REVERT: I 48 TYR cc_start: 0.9143 (m-80) cc_final: 0.8493 (m-80) REVERT: I 49 MET cc_start: 0.9224 (ttp) cc_final: 0.8938 (tmm) REVERT: I 57 GLU cc_start: 0.8634 (tp30) cc_final: 0.8343 (pt0) REVERT: J 55 PHE cc_start: 0.9142 (m-80) cc_final: 0.8917 (m-80) REVERT: K 48 TYR cc_start: 0.9415 (m-80) cc_final: 0.8799 (m-80) REVERT: K 53 ILE cc_start: 0.9584 (mm) cc_final: 0.8708 (tp) REVERT: K 57 GLU cc_start: 0.9215 (tp30) cc_final: 0.8567 (pt0) REVERT: L 26 ILE cc_start: 0.9766 (mt) cc_final: 0.9439 (tt) REVERT: L 29 SER cc_start: 0.9585 (t) cc_final: 0.9280 (p) REVERT: L 33 GLN cc_start: 0.9472 (tt0) cc_final: 0.9131 (mm110) REVERT: L 48 TYR cc_start: 0.8786 (m-80) cc_final: 0.8018 (m-80) REVERT: L 62 PHE cc_start: 0.8652 (m-10) cc_final: 0.8447 (m-80) REVERT: M 1 MET cc_start: 0.7593 (mmp) cc_final: 0.7338 (mmp) REVERT: M 41 ILE cc_start: 0.8844 (tp) cc_final: 0.8268 (tt) REVERT: N 15 LEU cc_start: 0.9011 (mt) cc_final: 0.8070 (tp) REVERT: N 43 ASN cc_start: 0.8985 (p0) cc_final: 0.8718 (p0) REVERT: N 51 ILE cc_start: 0.9299 (mt) cc_final: 0.8659 (tt) REVERT: N 55 PHE cc_start: 0.9216 (m-10) cc_final: 0.8790 (m-80) REVERT: N 66 ILE cc_start: 0.9356 (mm) cc_final: 0.9129 (mm) REVERT: O 18 ILE cc_start: 0.9207 (mt) cc_final: 0.8607 (mt) REVERT: O 50 PHE cc_start: 0.8991 (m-10) cc_final: 0.8706 (m-80) REVERT: O 57 GLU cc_start: 0.9489 (tp30) cc_final: 0.8802 (tp30) REVERT: O 62 PHE cc_start: 0.9152 (m-80) cc_final: 0.8947 (m-80) REVERT: P 27 ILE cc_start: 0.9186 (mt) cc_final: 0.8950 (mt) REVERT: P 59 LEU cc_start: 0.9502 (mm) cc_final: 0.9232 (mm) REVERT: P 62 PHE cc_start: 0.9156 (m-80) cc_final: 0.8822 (m-80) REVERT: Q 1 MET cc_start: 0.6327 (mmm) cc_final: 0.5887 (mmp) REVERT: Q 18 ILE cc_start: 0.8643 (mt) cc_final: 0.8395 (mt) REVERT: Q 50 PHE cc_start: 0.9417 (m-80) cc_final: 0.9176 (m-80) REVERT: Q 68 PHE cc_start: 0.8962 (m-80) cc_final: 0.8633 (m-80) REVERT: T 244 PHE cc_start: 0.9047 (m-80) cc_final: 0.8746 (m-80) REVERT: T 264 MET cc_start: 0.8994 (mmt) cc_final: 0.8760 (tpp) REVERT: T 286 ILE cc_start: 0.9503 (pt) cc_final: 0.9267 (pt) REVERT: Z 206 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8962 (mm-30) REVERT: Z 280 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8751 (tm-30) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.0987 time to fit residues: 55.4941 Evaluate side-chains 306 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 154 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 HIS T 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.079776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.062977 restraints weight = 91548.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.064246 restraints weight = 64000.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.065162 restraints weight = 49278.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065756 restraints weight = 40602.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066222 restraints weight = 35450.351| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5040 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= 0.150 Angle : 0.654 10.496 17946 Z= 0.343 Chirality : 0.045 0.451 2226 Planarity : 0.005 0.066 2320 Dihedral : 3.904 16.680 1945 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.19), residues: 1830 helix: 1.53 (0.13), residues: 1514 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 119 TYR 0.015 0.001 TYR Z 277 PHE 0.031 0.002 PHE O 62 TRP 0.008 0.001 TRP T 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00331 (13180) covalent geometry : angle 0.65439 (17942) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.40932 ( 4) hydrogen bonds : bond 0.04400 ( 1284) hydrogen bonds : angle 3.89124 ( 3831) ********************** 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 358 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 34 MET cc_start: 0.9107 (mmp) cc_final: 0.8761 (mmm) REVERT: Y 90 GLN cc_start: 0.9029 (mp10) cc_final: 0.8770 (mp10) REVERT: Y 117 ARG cc_start: 0.9377 (tmm-80) cc_final: 0.9080 (ttp80) REVERT: Y 120 MET cc_start: 0.7356 (tpt) cc_final: 0.6597 (ttt) REVERT: V 82 GLN cc_start: 0.9404 (tp-100) cc_final: 0.9083 (tp-100) REVERT: H 29 SER cc_start: 0.9351 (t) cc_final: 0.9100 (m) REVERT: H 49 MET cc_start: 0.9109 (ppp) cc_final: 0.8585 (ppp) REVERT: H 50 PHE cc_start: 0.8846 (m-80) cc_final: 0.8568 (m-10) REVERT: H 53 ILE cc_start: 0.8952 (tp) cc_final: 0.8581 (tp) REVERT: H 62 PHE cc_start: 0.9153 (m-10) cc_final: 0.8767 (m-80) REVERT: I 1 MET cc_start: 0.8297 (mtp) cc_final: 0.7733 (ttt) REVERT: I 29 SER cc_start: 0.9332 (t) cc_final: 0.9069 (p) REVERT: I 48 TYR cc_start: 0.9139 (m-80) cc_final: 0.8480 (m-80) REVERT: I 49 MET cc_start: 0.9163 (ttp) cc_final: 0.8786 (tmm) REVERT: I 57 GLU cc_start: 0.8633 (tp30) cc_final: 0.8321 (pt0) REVERT: J 26 ILE cc_start: 0.9511 (tp) cc_final: 0.9309 (tp) REVERT: K 48 TYR cc_start: 0.9380 (m-80) cc_final: 0.8949 (m-80) REVERT: K 49 MET cc_start: 0.9422 (ppp) cc_final: 0.9166 (ppp) REVERT: K 53 ILE cc_start: 0.9585 (mm) cc_final: 0.9166 (mm) REVERT: K 57 GLU cc_start: 0.9141 (tp30) cc_final: 0.8554 (pt0) REVERT: L 26 ILE cc_start: 0.9756 (mt) cc_final: 0.9464 (tt) REVERT: L 29 SER cc_start: 0.9547 (t) cc_final: 0.9243 (p) REVERT: L 33 GLN cc_start: 0.9489 (tt0) cc_final: 0.9119 (mm110) REVERT: L 48 TYR cc_start: 0.8819 (m-80) cc_final: 0.8033 (m-80) REVERT: L 55 PHE cc_start: 0.9242 (m-80) cc_final: 0.8864 (m-80) REVERT: L 62 PHE cc_start: 0.8653 (m-10) cc_final: 0.8447 (m-80) REVERT: M 1 MET cc_start: 0.7621 (mmp) cc_final: 0.7240 (mmp) REVERT: M 41 ILE cc_start: 0.8801 (tp) cc_final: 0.8330 (tt) REVERT: N 15 LEU cc_start: 0.9104 (mt) cc_final: 0.8278 (tp) REVERT: N 43 ASN cc_start: 0.8946 (p0) cc_final: 0.8679 (p0) REVERT: N 51 ILE cc_start: 0.9301 (mt) cc_final: 0.8657 (tt) REVERT: N 55 PHE cc_start: 0.9183 (m-10) cc_final: 0.8705 (m-80) REVERT: N 66 ILE cc_start: 0.9345 (mm) cc_final: 0.9135 (mm) REVERT: O 18 ILE cc_start: 0.9168 (mt) cc_final: 0.8556 (mt) REVERT: O 50 PHE cc_start: 0.8969 (m-10) cc_final: 0.8659 (m-80) REVERT: O 57 GLU cc_start: 0.9502 (tp30) cc_final: 0.8890 (tp30) REVERT: O 62 PHE cc_start: 0.9188 (m-80) cc_final: 0.8975 (m-80) REVERT: P 27 ILE cc_start: 0.9184 (mt) cc_final: 0.8942 (mt) REVERT: P 55 PHE cc_start: 0.9013 (m-80) cc_final: 0.8259 (m-80) REVERT: P 59 LEU cc_start: 0.9498 (mm) cc_final: 0.9230 (mm) REVERT: P 62 PHE cc_start: 0.9181 (m-80) cc_final: 0.8843 (m-80) REVERT: P 64 LEU cc_start: 0.9664 (mt) cc_final: 0.9366 (mt) REVERT: P 68 PHE cc_start: 0.9217 (m-80) cc_final: 0.8552 (m-80) REVERT: Q 1 MET cc_start: 0.6242 (mmm) cc_final: 0.5805 (mmp) REVERT: Q 18 ILE cc_start: 0.8505 (mt) cc_final: 0.8250 (mt) REVERT: Q 50 PHE cc_start: 0.9403 (m-80) cc_final: 0.9163 (m-80) REVERT: Q 68 PHE cc_start: 0.8970 (m-80) cc_final: 0.8569 (m-80) REVERT: T 244 PHE cc_start: 0.9060 (m-80) cc_final: 0.8763 (m-80) REVERT: T 264 MET cc_start: 0.8964 (mmt) cc_final: 0.8562 (tpt) REVERT: T 286 ILE cc_start: 0.9492 (pt) cc_final: 0.9284 (pt) REVERT: Z 206 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8979 (mm-30) REVERT: Z 280 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8696 (tm-30) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.0887 time to fit residues: 48.8706 Evaluate side-chains 305 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 115 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.075703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.059412 restraints weight = 90285.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060535 restraints weight = 63954.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061274 restraints weight = 49867.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061817 restraints weight = 41859.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.062030 restraints weight = 36860.512| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13182 Z= 0.246 Angle : 0.707 10.256 17946 Z= 0.387 Chirality : 0.047 0.374 2226 Planarity : 0.005 0.066 2320 Dihedral : 4.096 18.852 1945 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.19), residues: 1830 helix: 1.34 (0.13), residues: 1510 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 37 TYR 0.023 0.002 TYR Z 277 PHE 0.037 0.003 PHE I 62 TRP 0.018 0.002 TRP T 208 HIS 0.004 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00521 (13180) covalent geometry : angle 0.70741 (17942) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.41233 ( 4) hydrogen bonds : bond 0.04804 ( 1284) hydrogen bonds : angle 4.15062 ( 3831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.59 seconds wall clock time: 47 minutes 10.30 seconds (2830.30 seconds total)