Starting phenix.real_space_refine on Thu Feb 5 13:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qwu_53428/02_2026/9qwu_53428.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qwu_53428/02_2026/9qwu_53428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qwu_53428/02_2026/9qwu_53428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qwu_53428/02_2026/9qwu_53428.map" model { file = "/net/cci-nas-00/data/ceres_data/9qwu_53428/02_2026/9qwu_53428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qwu_53428/02_2026/9qwu_53428.cif" } resolution = 3.1 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 97 5.16 5 C 10794 2.51 5 N 2941 2.21 5 O 3197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17031 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1058 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7442 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 34, 'TRANS': 912} Chain breaks: 6 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "B" Number of atoms: 7400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 942, 7400 Classifications: {'peptide': 942} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 34, 'TRANS': 907} Chain breaks: 7 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "F" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 485 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 7, 'GLU:plan': 16, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 193 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3152 SG CYS A3532 50.460 67.103 60.511 1.00 93.57 S ATOM 3173 SG CYS A3535 52.954 69.765 59.436 1.00 68.65 S ATOM 5152 SG CYS A3872 53.756 67.372 62.344 1.00 62.65 S ATOM 5174 SG CYS A3875 50.964 70.042 62.664 1.00 69.77 S ATOM 10916 SG CYS B3532 106.796 82.465 60.659 1.00 84.57 S ATOM 10937 SG CYS B3535 104.336 79.833 59.521 1.00 65.08 S ATOM 12916 SG CYS B3872 103.571 82.118 62.498 1.00 69.83 S ATOM 12938 SG CYS B3875 106.391 79.432 62.736 1.00 74.63 S Time building chain proxies: 4.02, per 1000 atoms: 0.24 Number of scatterers: 17031 At special positions: 0 Unit cell: (157.232, 150.892, 134.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 97 16.00 O 3197 8.00 N 2941 7.00 C 10794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.55 Conformation dependent library (CDL) restraints added in 790.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5201 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3532 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3535 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3875 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3872 " pdb=" ZN B5201 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3532 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3535 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3875 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3872 " Number of angles added : 12 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 9 sheets defined 71.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 32 through 40 removed outlier: 3.570A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.501A pdb=" N VAL E 56 " --> pdb=" O MET E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'A' and resid 3224 through 3247 removed outlier: 3.654A pdb=" N GLN A3247 " --> pdb=" O LEU A3243 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3286 removed outlier: 3.627A pdb=" N HIS A3275 " --> pdb=" O SER A3271 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3297 removed outlier: 3.922A pdb=" N TRP A3290 " --> pdb=" O ARG A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3308 Processing helix chain 'A' and resid 3315 through 3328 Processing helix chain 'A' and resid 3329 through 3338 removed outlier: 3.735A pdb=" N LEU A3333 " --> pdb=" O GLY A3329 " (cutoff:3.500A) Processing helix chain 'A' and resid 3388 through 3403 Processing helix chain 'A' and resid 3404 through 3417 removed outlier: 3.545A pdb=" N LEU A3417 " --> pdb=" O ARG A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3438 removed outlier: 3.719A pdb=" N ARG A3425 " --> pdb=" O SER A3421 " (cutoff:3.500A) Processing helix chain 'A' and resid 3440 through 3455 Processing helix chain 'A' and resid 3456 through 3464 Proline residue: A3459 - end of helix removed outlier: 3.705A pdb=" N GLY A3462 " --> pdb=" O PRO A3459 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A3463 " --> pdb=" O ALA A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3479 Processing helix chain 'A' and resid 3482 through 3506 Processing helix chain 'A' and resid 3509 through 3518 removed outlier: 4.367A pdb=" N GLY A3518 " --> pdb=" O ASN A3514 " (cutoff:3.500A) Processing helix chain 'A' and resid 3532 through 3537 Processing helix chain 'A' and resid 3547 through 3550 No H-bonds generated for 'chain 'A' and resid 3547 through 3550' Processing helix chain 'A' and resid 3728 through 3755 Processing helix chain 'A' and resid 3756 through 3770 removed outlier: 3.540A pdb=" N GLU A3769 " --> pdb=" O CYS A3765 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A3770 " --> pdb=" O LYS A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3805 Processing helix chain 'A' and resid 3806 through 3843 removed outlier: 4.017A pdb=" N SER A3843 " --> pdb=" O ALA A3839 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3860 Processing helix chain 'A' and resid 3861 through 3864 removed outlier: 3.811A pdb=" N CYS A3864 " --> pdb=" O VAL A3861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3861 through 3864' Processing helix chain 'A' and resid 3872 through 3891 Processing helix chain 'A' and resid 3893 through 3904 Processing helix chain 'A' and resid 3904 through 3912 removed outlier: 3.694A pdb=" N GLU A3908 " --> pdb=" O GLY A3904 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3932 Processing helix chain 'A' and resid 3936 through 3957 removed outlier: 4.024A pdb=" N GLY A3957 " --> pdb=" O THR A3953 " (cutoff:3.500A) Processing helix chain 'A' and resid 3961 through 3967 removed outlier: 4.314A pdb=" N ALA A3965 " --> pdb=" O ASN A3961 " (cutoff:3.500A) Processing helix chain 'A' and resid 3968 through 3981 removed outlier: 3.765A pdb=" N LYS A3981 " --> pdb=" O ASP A3977 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4000 removed outlier: 3.651A pdb=" N ARG A3989 " --> pdb=" O CYS A3985 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4012 Processing helix chain 'A' and resid 4012 through 4025 Processing helix chain 'A' and resid 4038 through 4042 Processing helix chain 'A' and resid 4055 through 4060 Processing helix chain 'A' and resid 4061 through 4062 No H-bonds generated for 'chain 'A' and resid 4061 through 4062' Processing helix chain 'A' and resid 4063 through 4066 Processing helix chain 'A' and resid 4067 through 4074 removed outlier: 3.531A pdb=" N CYS A4074 " --> pdb=" O ALA A4070 " (cutoff:3.500A) Processing helix chain 'A' and resid 4088 through 4113 Processing helix chain 'A' and resid 4128 through 4134 removed outlier: 3.585A pdb=" N PHE A4134 " --> pdb=" O ARG A4130 " (cutoff:3.500A) Processing helix chain 'A' and resid 4138 through 4152 removed outlier: 3.942A pdb=" N ARG A4142 " --> pdb=" O THR A4138 " (cutoff:3.500A) Processing helix chain 'A' and resid 4155 through 4169 removed outlier: 3.868A pdb=" N GLN A4161 " --> pdb=" O SER A4157 " (cutoff:3.500A) Processing helix chain 'A' and resid 4170 through 4173 Processing helix chain 'A' and resid 4177 through 4179 No H-bonds generated for 'chain 'A' and resid 4177 through 4179' Processing helix chain 'A' and resid 4180 through 4191 Processing helix chain 'A' and resid 4193 through 4203 removed outlier: 3.546A pdb=" N LYS A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4204 through 4227 removed outlier: 4.047A pdb=" N TYR A4208 " --> pdb=" O GLY A4204 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A4226 " --> pdb=" O ALA A4222 " (cutoff:3.500A) Processing helix chain 'A' and resid 4235 through 4251 removed outlier: 4.288A pdb=" N VAL A4251 " --> pdb=" O SER A4247 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4258 Processing helix chain 'A' and resid 4262 through 4276 removed outlier: 3.595A pdb=" N LEU A4276 " --> pdb=" O CYS A4272 " (cutoff:3.500A) Processing helix chain 'A' and resid 4281 through 4299 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 303 through 327 removed outlier: 3.626A pdb=" N THR C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 3224 through 3247 removed outlier: 3.793A pdb=" N GLN B3247 " --> pdb=" O LEU B3243 " (cutoff:3.500A) Processing helix chain 'B' and resid 3265 through 3286 removed outlier: 3.610A pdb=" N HIS B3275 " --> pdb=" O SER B3271 " (cutoff:3.500A) Processing helix chain 'B' and resid 3286 through 3297 removed outlier: 3.895A pdb=" N TRP B3290 " --> pdb=" O ARG B3286 " (cutoff:3.500A) Processing helix chain 'B' and resid 3300 through 3308 Processing helix chain 'B' and resid 3315 through 3328 Processing helix chain 'B' and resid 3329 through 3338 removed outlier: 3.735A pdb=" N LEU B3333 " --> pdb=" O GLY B3329 " (cutoff:3.500A) Processing helix chain 'B' and resid 3388 through 3403 Processing helix chain 'B' and resid 3404 through 3417 removed outlier: 3.714A pdb=" N LEU B3417 " --> pdb=" O ARG B3413 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3438 removed outlier: 3.569A pdb=" N ARG B3425 " --> pdb=" O SER B3421 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B3438 " --> pdb=" O HIS B3434 " (cutoff:3.500A) Processing helix chain 'B' and resid 3440 through 3455 Processing helix chain 'B' and resid 3456 through 3464 Proline residue: B3459 - end of helix removed outlier: 3.744A pdb=" N GLY B3462 " --> pdb=" O PRO B3459 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ARG B3463 " --> pdb=" O ALA B3460 " (cutoff:3.500A) Processing helix chain 'B' and resid 3465 through 3479 Processing helix chain 'B' and resid 3482 through 3506 Processing helix chain 'B' and resid 3509 through 3518 removed outlier: 4.317A pdb=" N GLY B3518 " --> pdb=" O ASN B3514 " (cutoff:3.500A) Processing helix chain 'B' and resid 3532 through 3537 Processing helix chain 'B' and resid 3547 through 3550 No H-bonds generated for 'chain 'B' and resid 3547 through 3550' Processing helix chain 'B' and resid 3728 through 3755 Processing helix chain 'B' and resid 3756 through 3770 removed outlier: 3.562A pdb=" N GLU B3769 " --> pdb=" O CYS B3765 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B3770 " --> pdb=" O LYS B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3788 through 3792 removed outlier: 3.980A pdb=" N VAL B3792 " --> pdb=" O SER B3789 " (cutoff:3.500A) Processing helix chain 'B' and resid 3793 through 3806 removed outlier: 3.665A pdb=" N ASP B3806 " --> pdb=" O GLU B3802 " (cutoff:3.500A) Processing helix chain 'B' and resid 3806 through 3843 removed outlier: 3.544A pdb=" N SER B3842 " --> pdb=" O ALA B3838 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER B3843 " --> pdb=" O ALA B3839 " (cutoff:3.500A) Processing helix chain 'B' and resid 3853 through 3860 Processing helix chain 'B' and resid 3861 through 3864 removed outlier: 3.696A pdb=" N CYS B3864 " --> pdb=" O VAL B3861 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3861 through 3864' Processing helix chain 'B' and resid 3872 through 3891 Processing helix chain 'B' and resid 3893 through 3904 removed outlier: 3.549A pdb=" N GLY B3904 " --> pdb=" O LEU B3900 " (cutoff:3.500A) Processing helix chain 'B' and resid 3904 through 3912 removed outlier: 3.677A pdb=" N GLU B3908 " --> pdb=" O GLY B3904 " (cutoff:3.500A) Processing helix chain 'B' and resid 3918 through 3932 Processing helix chain 'B' and resid 3936 through 3957 removed outlier: 3.949A pdb=" N GLY B3957 " --> pdb=" O THR B3953 " (cutoff:3.500A) Processing helix chain 'B' and resid 3961 through 3967 removed outlier: 4.349A pdb=" N ALA B3965 " --> pdb=" O ASN B3961 " (cutoff:3.500A) Processing helix chain 'B' and resid 3968 through 3981 removed outlier: 3.611A pdb=" N LYS B3981 " --> pdb=" O ASP B3977 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4000 removed outlier: 3.605A pdb=" N ARG B3989 " --> pdb=" O CYS B3985 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4012 Processing helix chain 'B' and resid 4012 through 4025 Processing helix chain 'B' and resid 4038 through 4043 removed outlier: 4.050A pdb=" N THR B4043 " --> pdb=" O GLU B4040 " (cutoff:3.500A) Processing helix chain 'B' and resid 4055 through 4060 Processing helix chain 'B' and resid 4061 through 4062 No H-bonds generated for 'chain 'B' and resid 4061 through 4062' Processing helix chain 'B' and resid 4063 through 4066 Processing helix chain 'B' and resid 4067 through 4074 Processing helix chain 'B' and resid 4088 through 4110 Processing helix chain 'B' and resid 4127 through 4134 removed outlier: 4.360A pdb=" N GLN B4131 " --> pdb=" O ASN B4127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B4134 " --> pdb=" O ARG B4130 " (cutoff:3.500A) Processing helix chain 'B' and resid 4138 through 4152 removed outlier: 3.915A pdb=" N ARG B4142 " --> pdb=" O THR B4138 " (cutoff:3.500A) Processing helix chain 'B' and resid 4155 through 4169 removed outlier: 3.805A pdb=" N GLN B4161 " --> pdb=" O SER B4157 " (cutoff:3.500A) Processing helix chain 'B' and resid 4170 through 4173 Processing helix chain 'B' and resid 4177 through 4179 No H-bonds generated for 'chain 'B' and resid 4177 through 4179' Processing helix chain 'B' and resid 4180 through 4191 removed outlier: 3.647A pdb=" N LYS B4189 " --> pdb=" O ALA B4185 " (cutoff:3.500A) Processing helix chain 'B' and resid 4193 through 4203 removed outlier: 3.630A pdb=" N LYS B4197 " --> pdb=" O SER B4193 " (cutoff:3.500A) Processing helix chain 'B' and resid 4205 through 4227 Processing helix chain 'B' and resid 4235 through 4251 removed outlier: 4.614A pdb=" N VAL B4251 " --> pdb=" O SER B4247 " (cutoff:3.500A) Processing helix chain 'B' and resid 4251 through 4258 Processing helix chain 'B' and resid 4258 through 4276 removed outlier: 3.756A pdb=" N LEU B4262 " --> pdb=" O PHE B4258 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR B4265 " --> pdb=" O ARG B4261 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B4276 " --> pdb=" O CYS B4272 " (cutoff:3.500A) Processing helix chain 'B' and resid 4281 through 4299 Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.730A pdb=" N LEU D 296 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 326 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 32 through 40 removed outlier: 3.732A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 84 through 94 Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 118 through 129 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 3249 through 3251 Processing sheet with id=AA3, first strand: chain 'A' and resid 3543 through 3546 removed outlier: 3.970A pdb=" N LYS A3573 " --> pdb=" O TYR A3716 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A3553 " --> pdb=" O LYS A3564 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A3566 " --> pdb=" O LYS A3551 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N LYS A3551 " --> pdb=" O ILE A3566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3543 through 3546 removed outlier: 3.970A pdb=" N LYS A3573 " --> pdb=" O TYR A3716 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N VAL A3563 " --> pdb=" O GLU A3643 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N GLU A3643 " --> pdb=" O VAL A3563 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N LEU A3565 " --> pdb=" O MET A3641 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N MET A3641 " --> pdb=" O LEU A3565 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N GLY A3567 " --> pdb=" O ASN A3639 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN A3639 " --> pdb=" O GLY A3567 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LYS A3573 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 10.828A pdb=" N LEU A3633 " --> pdb=" O LYS A3573 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR A3575 " --> pdb=" O LEU A3631 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N LEU A3631 " --> pdb=" O THR A3575 " (cutoff:3.500A) removed outlier: 10.638A pdb=" N LYS A3577 " --> pdb=" O ILE A3629 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N ILE A3629 " --> pdb=" O LYS A3577 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A3592 " --> pdb=" O ALA A3615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 4051 through 4052 Processing sheet with id=AA6, first strand: chain 'B' and resid 3249 through 3251 Processing sheet with id=AA7, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 3.915A pdb=" N LYS B3573 " --> pdb=" O TYR B3716 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B3553 " --> pdb=" O LYS B3564 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE B3566 " --> pdb=" O LYS B3551 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N LYS B3551 " --> pdb=" O ILE B3566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 3.915A pdb=" N LYS B3573 " --> pdb=" O TYR B3716 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN B3560 " --> pdb=" O GLU B3643 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B3643 " --> pdb=" O GLN B3560 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B3562 " --> pdb=" O MET B3641 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET B3641 " --> pdb=" O VAL B3562 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B3564 " --> pdb=" O ASN B3639 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B3639 " --> pdb=" O LYS B3564 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B3566 " --> pdb=" O ALA B3637 " (cutoff:3.500A) removed outlier: 11.254A pdb=" N ALA B3637 " --> pdb=" O ILE B3566 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N SER B3568 " --> pdb=" O ILE B3635 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ILE B3635 " --> pdb=" O SER B3568 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N THR B3570 " --> pdb=" O LEU B3633 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LEU B3633 " --> pdb=" O THR B3570 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER B3572 " --> pdb=" O LEU B3631 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B3592 " --> pdb=" O ALA B3615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4051 through 4052 1117 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 1.99 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: 5607 1.34 - 1.46: 3680 1.46 - 1.58: 7871 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 17296 Sorted by residual: bond pdb=" CB GLU B4216 " pdb=" CG GLU B4216 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CG ARG E 38 " pdb=" CD ARG E 38 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CA VAL A3540 " pdb=" CB VAL A3540 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.29e-02 6.01e+03 1.53e+00 bond pdb=" CB PHE A4108 " pdb=" CG PHE A4108 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.30e-02 1.89e+03 1.27e+00 bond pdb=" CG GLU B4216 " pdb=" CD GLU B4216 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.23e+00 ... (remaining 17291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 23307 2.86 - 5.73: 106 5.73 - 8.59: 6 8.59 - 11.46: 2 11.46 - 14.32: 1 Bond angle restraints: 23422 Sorted by residual: angle pdb=" CA LEU B4097 " pdb=" CB LEU B4097 " pdb=" CG LEU B4097 " ideal model delta sigma weight residual 116.30 130.62 -14.32 3.50e+00 8.16e-02 1.67e+01 angle pdb=" N ILE E 131 " pdb=" CA ILE E 131 " pdb=" C ILE E 131 " ideal model delta sigma weight residual 112.96 108.89 4.07 1.00e+00 1.00e+00 1.66e+01 angle pdb=" CB MET E 52 " pdb=" CG MET E 52 " pdb=" SD MET E 52 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CA ARG E 38 " pdb=" CB ARG E 38 " pdb=" CG ARG E 38 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CG ARG E 38 " pdb=" CD ARG E 38 " pdb=" NE ARG E 38 " ideal model delta sigma weight residual 112.00 105.15 6.85 2.20e+00 2.07e-01 9.68e+00 ... (remaining 23417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9144 17.94 - 35.89: 1121 35.89 - 53.83: 268 53.83 - 71.77: 41 71.77 - 89.72: 20 Dihedral angle restraints: 10594 sinusoidal: 4110 harmonic: 6484 Sorted by residual: dihedral pdb=" CA ALA B4176 " pdb=" C ALA B4176 " pdb=" N GLY B4177 " pdb=" CA GLY B4177 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLU E 115 " pdb=" C GLU E 115 " pdb=" N LYS E 116 " pdb=" CA LYS E 116 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA VAL B4251 " pdb=" C VAL B4251 " pdb=" N GLU B4252 " pdb=" CA GLU B4252 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 10591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2202 0.045 - 0.091: 479 0.091 - 0.136: 94 0.136 - 0.182: 1 0.182 - 0.227: 2 Chirality restraints: 2778 Sorted by residual: chirality pdb=" CB THR A4098 " pdb=" CA THR A4098 " pdb=" OG1 THR A4098 " pdb=" CG2 THR A4098 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN A3537 " pdb=" N ASN A3537 " pdb=" C ASN A3537 " pdb=" CB ASN A3537 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE A4155 " pdb=" CA ILE A4155 " pdb=" CG1 ILE A4155 " pdb=" CG2 ILE A4155 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2775 not shown) Planarity restraints: 2959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A4108 " -0.013 2.00e-02 2.50e+03 1.77e-02 5.47e+00 pdb=" CG PHE A4108 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A4108 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A4108 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A4108 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A4108 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A4108 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A3537 " -0.011 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C ASN A3537 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A3537 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A3538 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A4155 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A4156 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A4156 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A4156 " -0.023 5.00e-02 4.00e+02 ... (remaining 2956 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 163 2.70 - 3.25: 16550 3.25 - 3.80: 26667 3.80 - 4.35: 32374 4.35 - 4.90: 55076 Nonbonded interactions: 130830 Sorted by model distance: nonbonded pdb=" O ASN A3537 " pdb=" ND2 ASN A3537 " model vdw 2.146 3.120 nonbonded pdb=" O ASN A4126 " pdb=" OD1 ASN A4126 " model vdw 2.460 3.040 nonbonded pdb=" N THR E 27 " pdb=" OG1 THR E 27 " model vdw 2.531 2.496 nonbonded pdb=" O GLU A4040 " pdb=" OE1 GLU A4040 " model vdw 2.540 3.040 nonbonded pdb=" N GLN E 9 " pdb=" OE1 GLN E 9 " model vdw 2.560 3.120 ... (remaining 130825 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 'A' and (resid 3223 through 4110 or resid 4116 through 5201)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.600 Find NCS groups from input model: 0.290 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.004 0.040 17304 Z= 0.182 Angle : 0.586 14.323 23434 Z= 0.314 Chirality : 0.039 0.227 2778 Planarity : 0.004 0.042 2959 Dihedral : 16.739 89.716 6352 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.37 % Allowed : 18.74 % Favored : 79.89 % 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 are not related in a simple way. whole: 1.99 (0.18), residues: 2146 helix: 2.22 (0.14), residues: 1431 sheet: 1.25 (0.59), residues: 76 loop : -0.79 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 38 TYR 0.015 0.002 TYR B3556 PHE 0.041 0.002 PHE A4108 TRP 0.019 0.001 TRP B3959 HIS 0.008 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00429 (17296) covalent geometry : angle 0.58316 (23422) hydrogen bonds : bond 0.12784 ( 1099) hydrogen bonds : angle 4.78243 ( 3258) metal coordination : bond 0.00627 ( 8) metal coordination : angle 2.63646 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.701 Fit side-chains REVERT: E 43 ASN cc_start: 0.7877 (m110) cc_final: 0.7048 (m-40) REVERT: E 115 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6650 (tt0) REVERT: E 128 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: A 3228 ARG cc_start: 0.7718 (mtp85) cc_final: 0.6292 (ptt180) REVERT: A 3851 PHE cc_start: 0.7059 (m-80) cc_final: 0.6771 (m-80) REVERT: A 4103 TRP cc_start: 0.7516 (t60) cc_final: 0.6664 (t-100) REVERT: A 4108 PHE cc_start: 0.7989 (t80) cc_final: 0.7261 (t80) REVERT: A 4122 LYS cc_start: 0.8184 (tptm) cc_final: 0.7758 (mmtp) REVERT: B 3504 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8641 (mt) REVERT: B 3774 LYS cc_start: 0.7540 (pttt) cc_final: 0.6408 (mmtt) REVERT: B 3794 ARG cc_start: 0.8732 (ptt180) cc_final: 0.8516 (ptt-90) outliers start: 25 outliers final: 20 residues processed: 184 average time/residue: 0.1465 time to fit residues: 40.4463 Evaluate side-chains 176 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3744 ASP Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4193 SER Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4229 SER Chi-restraints excluded: chain B residue 4277 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4126 ASN A4234 GLN B3560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107122 restraints weight = 25089.381| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.33 r_work: 0.3250 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17304 Z= 0.132 Angle : 0.472 8.289 23434 Z= 0.248 Chirality : 0.036 0.158 2778 Planarity : 0.004 0.039 2959 Dihedral : 5.080 55.469 2388 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.75 % Allowed : 17.75 % Favored : 79.51 % 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 are not related in a simple way. whole: 2.37 (0.18), residues: 2146 helix: 2.48 (0.14), residues: 1447 sheet: 1.25 (0.60), residues: 78 loop : -0.66 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 38 TYR 0.013 0.001 TYR A4101 PHE 0.026 0.001 PHE A4108 TRP 0.007 0.001 TRP B3959 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00310 (17296) covalent geometry : angle 0.47046 (23422) hydrogen bonds : bond 0.04332 ( 1099) hydrogen bonds : angle 3.44063 ( 3258) metal coordination : bond 0.00635 ( 8) metal coordination : angle 1.66353 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.752 Fit side-chains REVERT: A 3228 ARG cc_start: 0.7745 (mtp85) cc_final: 0.6340 (ptt180) REVERT: A 3537 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7740 (p0) REVERT: A 3851 PHE cc_start: 0.6889 (m-80) cc_final: 0.6636 (m-80) REVERT: A 4122 LYS cc_start: 0.8126 (tptm) cc_final: 0.7713 (mmtp) REVERT: B 3523 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (t0) REVERT: B 3714 MET cc_start: 0.6250 (tpp) cc_final: 0.5980 (tpp) REVERT: B 3774 LYS cc_start: 0.7595 (pttt) cc_final: 0.6504 (mmtt) REVERT: B 3924 GLU cc_start: 0.8974 (tp30) cc_final: 0.8753 (mm-30) outliers start: 50 outliers final: 27 residues processed: 210 average time/residue: 0.1401 time to fit residues: 45.2060 Evaluate side-chains 181 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 3318 VAL Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4214 THR Chi-restraints excluded: chain B residue 4217 ILE Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 180 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106996 restraints weight = 25100.833| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.58 r_work: 0.3226 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17304 Z= 0.134 Angle : 0.464 9.785 23434 Z= 0.242 Chirality : 0.036 0.160 2778 Planarity : 0.004 0.039 2959 Dihedral : 4.194 58.372 2362 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.30 % Allowed : 18.13 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.18), residues: 2146 helix: 2.54 (0.14), residues: 1447 sheet: 1.61 (0.63), residues: 70 loop : -0.72 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.013 0.001 TYR B4101 PHE 0.015 0.001 PHE A4108 TRP 0.008 0.001 TRP B3959 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00320 (17296) covalent geometry : angle 0.46307 (23422) hydrogen bonds : bond 0.04248 ( 1099) hydrogen bonds : angle 3.28647 ( 3258) metal coordination : bond 0.00550 ( 8) metal coordination : angle 1.62113 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.735 Fit side-chains REVERT: E 37 MET cc_start: 0.7644 (ptp) cc_final: 0.6928 (pmm) REVERT: E 38 ARG cc_start: 0.6213 (tpt90) cc_final: 0.5962 (tpp-160) REVERT: E 115 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: A 3228 ARG cc_start: 0.7805 (mtp85) cc_final: 0.6447 (ptt180) REVERT: A 3247 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: A 3537 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7606 (p0) REVERT: A 3714 MET cc_start: 0.6692 (mmm) cc_final: 0.6383 (mmt) REVERT: A 4122 LYS cc_start: 0.8006 (tptm) cc_final: 0.7594 (mmtp) REVERT: A 4244 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8145 (tp) REVERT: C 303 GLU cc_start: 0.6229 (tm-30) cc_final: 0.5843 (tm-30) REVERT: B 3504 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8529 (mt) REVERT: B 3523 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.8020 (t0) REVERT: B 3774 LYS cc_start: 0.7560 (pttt) cc_final: 0.6529 (mmtt) REVERT: B 3888 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8482 (ttp80) REVERT: B 3924 GLU cc_start: 0.8823 (tp30) cc_final: 0.8406 (mm-30) REVERT: B 4091 GLU cc_start: 0.5920 (tp30) cc_final: 0.5490 (tp30) REVERT: D 295 ARG cc_start: 0.7790 (mtt180) cc_final: 0.6780 (ptt180) outliers start: 60 outliers final: 34 residues processed: 211 average time/residue: 0.1550 time to fit residues: 48.8192 Evaluate side-chains 196 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4234 GLN Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3867 THR Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4184 LEU Chi-restraints excluded: chain B residue 4214 THR Chi-restraints excluded: chain B residue 4217 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 137 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3400 ASN A4234 GLN B3247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108496 restraints weight = 25160.098| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.39 r_work: 0.3229 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17304 Z= 0.121 Angle : 0.449 11.190 23434 Z= 0.234 Chirality : 0.036 0.172 2778 Planarity : 0.004 0.039 2959 Dihedral : 4.096 59.961 2361 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.52 % Allowed : 17.97 % Favored : 78.52 % 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 are not related in a simple way. whole: 2.51 (0.18), residues: 2146 helix: 2.63 (0.14), residues: 1447 sheet: 1.40 (0.63), residues: 72 loop : -0.70 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.012 0.001 TYR A4101 PHE 0.018 0.001 PHE A4108 TRP 0.006 0.001 TRP A3455 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00287 (17296) covalent geometry : angle 0.44810 (23422) hydrogen bonds : bond 0.04013 ( 1099) hydrogen bonds : angle 3.21377 ( 3258) metal coordination : bond 0.00491 ( 8) metal coordination : angle 1.57430 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.490 Fit side-chains REVERT: E 75 ARG cc_start: 0.7077 (mpp80) cc_final: 0.6781 (mpp80) REVERT: E 90 PHE cc_start: 0.7147 (t80) cc_final: 0.6401 (m-80) REVERT: E 115 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: E 142 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6889 (t80) REVERT: A 3228 ARG cc_start: 0.7808 (mtp85) cc_final: 0.6448 (ptt180) REVERT: A 3310 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8700 (mt) REVERT: A 3537 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7764 (p0) REVERT: A 3714 MET cc_start: 0.6719 (mmm) cc_final: 0.6417 (mmt) REVERT: A 3851 PHE cc_start: 0.6663 (m-80) cc_final: 0.6389 (m-80) REVERT: A 3871 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6872 (mptt) REVERT: A 4103 TRP cc_start: 0.7520 (t60) cc_final: 0.6666 (t-100) REVERT: A 4122 LYS cc_start: 0.7904 (tptm) cc_final: 0.7648 (mmtp) REVERT: C 303 GLU cc_start: 0.6152 (tm-30) cc_final: 0.5580 (tm-30) REVERT: B 3247 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: B 3504 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 3523 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8027 (t0) REVERT: B 3774 LYS cc_start: 0.7589 (pttt) cc_final: 0.6558 (mmtt) REVERT: B 3851 PHE cc_start: 0.6333 (m-80) cc_final: 0.5889 (m-80) REVERT: B 3888 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8492 (ttp80) REVERT: B 3924 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8404 (mm-30) REVERT: B 4091 GLU cc_start: 0.5940 (tp30) cc_final: 0.5531 (tp30) REVERT: D 295 ARG cc_start: 0.7805 (mtt180) cc_final: 0.6804 (ptt180) outliers start: 64 outliers final: 39 residues processed: 214 average time/residue: 0.1181 time to fit residues: 38.3695 Evaluate side-chains 208 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3318 VAL Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4234 GLN Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3867 THR Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4184 LEU Chi-restraints excluded: chain B residue 4214 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 172 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 131 optimal weight: 0.0060 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 161 optimal weight: 0.0040 chunk 209 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 GLN B3247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109561 restraints weight = 24925.074| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.49 r_work: 0.3258 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17304 Z= 0.093 Angle : 0.425 12.840 23434 Z= 0.220 Chirality : 0.035 0.182 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.947 58.473 2361 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.24 % Allowed : 17.75 % Favored : 79.01 % 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 are not related in a simple way. whole: 2.74 (0.19), residues: 2146 helix: 2.81 (0.14), residues: 1449 sheet: 1.26 (0.62), residues: 78 loop : -0.62 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3238 TYR 0.012 0.001 TYR B4101 PHE 0.020 0.001 PHE A4108 TRP 0.005 0.001 TRP A4059 HIS 0.005 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00205 (17296) covalent geometry : angle 0.42368 (23422) hydrogen bonds : bond 0.03488 ( 1099) hydrogen bonds : angle 3.07098 ( 3258) metal coordination : bond 0.00398 ( 8) metal coordination : angle 1.54537 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.516 Fit side-chains REVERT: E 38 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.6875 (ttm-80) REVERT: E 75 ARG cc_start: 0.7098 (mpp80) cc_final: 0.6706 (mpp80) REVERT: E 117 LEU cc_start: 0.8227 (mp) cc_final: 0.7602 (mp) REVERT: E 142 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6640 (t80) REVERT: E 146 MET cc_start: 0.6572 (mmt) cc_final: 0.6248 (mmp) REVERT: A 3228 ARG cc_start: 0.7804 (mtp85) cc_final: 0.6487 (ptt180) REVERT: A 3247 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: A 3310 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8729 (mt) REVERT: A 3401 LYS cc_start: 0.7914 (pttt) cc_final: 0.7341 (tmmt) REVERT: A 3537 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.7883 (p0) REVERT: A 3714 MET cc_start: 0.6769 (mmm) cc_final: 0.6368 (mmt) REVERT: A 3871 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6811 (mptt) REVERT: A 4103 TRP cc_start: 0.7498 (t60) cc_final: 0.6602 (t-100) REVERT: A 4122 LYS cc_start: 0.7895 (tptm) cc_final: 0.7650 (mmtp) REVERT: A 4244 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8304 (tp) REVERT: C 303 GLU cc_start: 0.6340 (tm-30) cc_final: 0.5382 (tm-30) REVERT: C 309 MET cc_start: 0.7706 (tmm) cc_final: 0.6974 (tmm) REVERT: B 3247 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 3504 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 3523 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.8005 (t0) REVERT: B 3774 LYS cc_start: 0.7587 (pttt) cc_final: 0.6579 (mmtt) REVERT: B 3851 PHE cc_start: 0.6237 (m-80) cc_final: 0.5910 (m-80) REVERT: B 3868 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7319 (t) REVERT: B 3888 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8443 (ttp80) REVERT: B 3924 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8365 (mm-30) REVERT: B 4091 GLU cc_start: 0.5966 (tp30) cc_final: 0.5549 (tp30) REVERT: D 295 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6793 (ptt180) outliers start: 59 outliers final: 29 residues processed: 214 average time/residue: 0.1227 time to fit residues: 40.0351 Evaluate side-chains 204 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3318 VAL Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3565 LEU Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4234 GLN Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3868 SER Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 0.5980 chunk 146 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 GLN B3247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108103 restraints weight = 25020.772| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.33 r_work: 0.3255 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17304 Z= 0.105 Angle : 0.430 13.446 23434 Z= 0.223 Chirality : 0.035 0.187 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.882 56.626 2359 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.63 % Allowed : 17.42 % Favored : 78.96 % 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 are not related in a simple way. whole: 2.75 (0.19), residues: 2146 helix: 2.81 (0.14), residues: 1449 sheet: 1.45 (0.64), residues: 72 loop : -0.62 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3238 TYR 0.012 0.001 TYR B4101 PHE 0.022 0.001 PHE A4108 TRP 0.006 0.001 TRP A4059 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00243 (17296) covalent geometry : angle 0.42865 (23422) hydrogen bonds : bond 0.03649 ( 1099) hydrogen bonds : angle 3.07262 ( 3258) metal coordination : bond 0.00407 ( 8) metal coordination : angle 1.64991 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 0.739 Fit side-chains REVERT: E 38 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.6900 (ttm-80) REVERT: E 75 ARG cc_start: 0.7184 (mpp80) cc_final: 0.6791 (mpp80) REVERT: E 90 PHE cc_start: 0.6669 (t80) cc_final: 0.6071 (m-80) REVERT: E 93 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: E 115 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: E 142 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6761 (t80) REVERT: E 146 MET cc_start: 0.6656 (mmt) cc_final: 0.6341 (mmp) REVERT: A 3228 ARG cc_start: 0.7842 (mtp85) cc_final: 0.6480 (ptt180) REVERT: A 3247 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: A 3310 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8770 (mt) REVERT: A 3401 LYS cc_start: 0.8008 (pttt) cc_final: 0.7400 (tmmt) REVERT: A 3537 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.7956 (p0) REVERT: A 3714 MET cc_start: 0.6733 (mmm) cc_final: 0.6303 (mmt) REVERT: A 3871 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7172 (mtmt) REVERT: A 4103 TRP cc_start: 0.7558 (t60) cc_final: 0.6628 (t-100) REVERT: A 4122 LYS cc_start: 0.7836 (tptm) cc_final: 0.7600 (mmtp) REVERT: A 4244 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8271 (tp) REVERT: C 303 GLU cc_start: 0.6354 (tm-30) cc_final: 0.5390 (tm-30) REVERT: B 3247 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: B 3504 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 3523 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8156 (t0) REVERT: B 3774 LYS cc_start: 0.7534 (pttt) cc_final: 0.6438 (mmtt) REVERT: B 3851 PHE cc_start: 0.6256 (m-80) cc_final: 0.5956 (m-80) REVERT: B 3868 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7221 (t) REVERT: B 3888 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8520 (ttp80) REVERT: B 3924 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: B 4091 GLU cc_start: 0.5722 (tp30) cc_final: 0.5318 (tp30) REVERT: B 4101 TYR cc_start: 0.7758 (m-80) cc_final: 0.7226 (m-10) REVERT: D 295 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6706 (ptt180) outliers start: 66 outliers final: 41 residues processed: 219 average time/residue: 0.1300 time to fit residues: 42.7787 Evaluate side-chains 218 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3270 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3318 VAL Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3914 LEU Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3868 SER Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 198 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108771 restraints weight = 24980.716| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.32 r_work: 0.3268 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17304 Z= 0.095 Angle : 0.432 14.136 23434 Z= 0.222 Chirality : 0.035 0.220 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.838 55.342 2359 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.35 % Allowed : 18.08 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.19), residues: 2146 helix: 2.86 (0.14), residues: 1451 sheet: 1.55 (0.65), residues: 70 loop : -0.57 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3228 TYR 0.012 0.001 TYR B4101 PHE 0.018 0.001 PHE A4108 TRP 0.005 0.001 TRP B3959 HIS 0.005 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00215 (17296) covalent geometry : angle 0.43024 (23422) hydrogen bonds : bond 0.03469 ( 1099) hydrogen bonds : angle 3.03446 ( 3258) metal coordination : bond 0.00384 ( 8) metal coordination : angle 1.62844 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.678 Fit side-chains REVERT: E 37 MET cc_start: 0.7860 (ptp) cc_final: 0.7010 (pmm) REVERT: E 38 ARG cc_start: 0.7696 (tpp-160) cc_final: 0.6961 (ttm-80) REVERT: E 75 ARG cc_start: 0.7188 (mpp80) cc_final: 0.6793 (mpp80) REVERT: E 90 PHE cc_start: 0.6641 (t80) cc_final: 0.6099 (m-80) REVERT: E 93 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6898 (m-10) REVERT: E 142 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6676 (t80) REVERT: E 146 MET cc_start: 0.6658 (mmt) cc_final: 0.6372 (mmp) REVERT: A 3228 ARG cc_start: 0.7840 (mtp85) cc_final: 0.6479 (ptt180) REVERT: A 3247 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: A 3310 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8780 (mt) REVERT: A 3401 LYS cc_start: 0.7996 (pttt) cc_final: 0.7414 (tmmt) REVERT: A 3537 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8032 (p0) REVERT: A 3714 MET cc_start: 0.6682 (mmm) cc_final: 0.6275 (mmt) REVERT: A 3871 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7189 (mtmt) REVERT: A 4103 TRP cc_start: 0.7650 (t60) cc_final: 0.6792 (t-100) REVERT: A 4122 LYS cc_start: 0.7815 (tptm) cc_final: 0.7576 (mmtp) REVERT: A 4244 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 303 GLU cc_start: 0.6465 (tm-30) cc_final: 0.5448 (tm-30) REVERT: C 309 MET cc_start: 0.7880 (tmm) cc_final: 0.7200 (tmm) REVERT: B 3247 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6701 (mp10) REVERT: B 3504 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8645 (mt) REVERT: B 3523 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8151 (t0) REVERT: B 3738 ASN cc_start: 0.8506 (t0) cc_final: 0.8191 (m110) REVERT: B 3774 LYS cc_start: 0.7523 (pttt) cc_final: 0.6425 (mmtt) REVERT: B 3851 PHE cc_start: 0.6252 (m-80) cc_final: 0.5979 (m-80) REVERT: B 3868 SER cc_start: 0.7505 (OUTLIER) cc_final: 0.7222 (t) REVERT: B 3888 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8499 (ttp80) REVERT: B 3924 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: B 4091 GLU cc_start: 0.5732 (tp30) cc_final: 0.5348 (tp30) REVERT: B 4101 TYR cc_start: 0.7717 (m-80) cc_final: 0.7183 (m-10) REVERT: B 4298 MET cc_start: 0.7047 (mtt) cc_final: 0.6715 (mtt) REVERT: D 295 ARG cc_start: 0.7838 (mtt180) cc_final: 0.6695 (ptt180) outliers start: 61 outliers final: 39 residues processed: 212 average time/residue: 0.1303 time to fit residues: 41.3166 Evaluate side-chains 217 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3270 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4092 LEU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4234 GLN Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3868 SER Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 157 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 133 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108827 restraints weight = 25010.002| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.33 r_work: 0.3270 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17304 Z= 0.095 Angle : 0.437 14.496 23434 Z= 0.223 Chirality : 0.035 0.223 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.793 53.538 2357 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.41 % Allowed : 18.08 % Favored : 78.52 % 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 are not related in a simple way. whole: 2.86 (0.19), residues: 2146 helix: 2.87 (0.14), residues: 1453 sheet: 1.14 (0.61), residues: 78 loop : -0.50 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3228 TYR 0.012 0.001 TYR A4101 PHE 0.025 0.001 PHE A4108 TRP 0.005 0.001 TRP B3959 HIS 0.005 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00216 (17296) covalent geometry : angle 0.43528 (23422) hydrogen bonds : bond 0.03423 ( 1099) hydrogen bonds : angle 3.01294 ( 3258) metal coordination : bond 0.00371 ( 8) metal coordination : angle 1.66719 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.666 Fit side-chains REVERT: E 37 MET cc_start: 0.7756 (ptp) cc_final: 0.6857 (pmm) REVERT: E 38 ARG cc_start: 0.7784 (tpp-160) cc_final: 0.7058 (ttm-80) REVERT: E 75 ARG cc_start: 0.7283 (mpp80) cc_final: 0.6904 (mpp80) REVERT: E 90 PHE cc_start: 0.6660 (t80) cc_final: 0.6046 (m-80) REVERT: E 93 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: E 142 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6566 (t80) REVERT: E 146 MET cc_start: 0.6688 (mmt) cc_final: 0.6443 (mmp) REVERT: A 3228 ARG cc_start: 0.7835 (mtp85) cc_final: 0.6475 (ptt180) REVERT: A 3247 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: A 3310 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8833 (mt) REVERT: A 3401 LYS cc_start: 0.7909 (pttt) cc_final: 0.7295 (tmmt) REVERT: A 3537 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8101 (p0) REVERT: A 3714 MET cc_start: 0.6755 (mmm) cc_final: 0.6365 (mmt) REVERT: A 3871 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7223 (mtmt) REVERT: A 4103 TRP cc_start: 0.7641 (t60) cc_final: 0.6769 (t-100) REVERT: A 4244 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8392 (tp) REVERT: C 303 GLU cc_start: 0.6484 (tm-30) cc_final: 0.5495 (tm-30) REVERT: C 309 MET cc_start: 0.7876 (tmm) cc_final: 0.7199 (tmm) REVERT: B 3247 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: B 3504 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 3523 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8009 (t0) REVERT: B 3738 ASN cc_start: 0.8497 (t0) cc_final: 0.8191 (m110) REVERT: B 3774 LYS cc_start: 0.7521 (pttt) cc_final: 0.6422 (mmtt) REVERT: B 3868 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.7195 (t) REVERT: B 3888 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8504 (ttp80) REVERT: B 3924 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8631 (mm-30) REVERT: B 4091 GLU cc_start: 0.5762 (tp30) cc_final: 0.5336 (tp30) REVERT: B 4101 TYR cc_start: 0.7696 (m-80) cc_final: 0.7127 (m-10) REVERT: B 4298 MET cc_start: 0.7059 (mtt) cc_final: 0.6736 (mtt) REVERT: D 295 ARG cc_start: 0.7852 (mtt180) cc_final: 0.6697 (ptt180) outliers start: 62 outliers final: 42 residues processed: 213 average time/residue: 0.1352 time to fit residues: 43.0155 Evaluate side-chains 221 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3270 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3629 ILE Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3851 PHE Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4092 LEU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3523 ASP Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3868 SER Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 206 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 193 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 GLN B3247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107524 restraints weight = 25077.956| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.32 r_work: 0.3249 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17304 Z= 0.118 Angle : 0.461 14.602 23434 Z= 0.236 Chirality : 0.036 0.216 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.863 51.040 2357 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.30 % Allowed : 18.30 % Favored : 78.41 % 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 are not related in a simple way. whole: 2.77 (0.19), residues: 2146 helix: 2.80 (0.14), residues: 1452 sheet: 1.29 (0.64), residues: 72 loop : -0.55 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3228 TYR 0.013 0.001 TYR A4101 PHE 0.022 0.001 PHE A4108 TRP 0.008 0.001 TRP B3959 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00280 (17296) covalent geometry : angle 0.45888 (23422) hydrogen bonds : bond 0.03786 ( 1099) hydrogen bonds : angle 3.08480 ( 3258) metal coordination : bond 0.00431 ( 8) metal coordination : angle 1.86060 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.600 Fit side-chains REVERT: E 38 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7130 (ttm-80) REVERT: E 75 ARG cc_start: 0.7258 (mpp80) cc_final: 0.6816 (mpp80) REVERT: E 93 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: E 115 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7290 (pt0) REVERT: E 142 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.6470 (t80) REVERT: E 146 MET cc_start: 0.6857 (mmt) cc_final: 0.6570 (mmp) REVERT: A 3228 ARG cc_start: 0.7850 (mtp85) cc_final: 0.6489 (ptt180) REVERT: A 3247 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: A 3310 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 3401 LYS cc_start: 0.7892 (pttt) cc_final: 0.7397 (tmmt) REVERT: A 3537 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8195 (p0) REVERT: A 3871 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6840 (mptt) REVERT: A 4103 TRP cc_start: 0.7683 (t60) cc_final: 0.6802 (t-100) REVERT: A 4244 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8260 (tp) REVERT: C 303 GLU cc_start: 0.6573 (tm-30) cc_final: 0.5560 (tm-30) REVERT: B 3247 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6748 (mp10) REVERT: B 3504 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 3738 ASN cc_start: 0.8521 (t0) cc_final: 0.8204 (m110) REVERT: B 3774 LYS cc_start: 0.7524 (pttt) cc_final: 0.6411 (mmtt) REVERT: B 3851 PHE cc_start: 0.6109 (m-80) cc_final: 0.5737 (m-80) REVERT: B 3868 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.7194 (t) REVERT: B 3888 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (ttp80) REVERT: B 3924 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8634 (mm-30) REVERT: B 4091 GLU cc_start: 0.5959 (tp30) cc_final: 0.5395 (tp30) REVERT: B 4101 TYR cc_start: 0.7701 (m-80) cc_final: 0.7149 (m-10) REVERT: D 295 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6699 (ptt180) outliers start: 60 outliers final: 44 residues processed: 212 average time/residue: 0.1425 time to fit residues: 45.1604 Evaluate side-chains 222 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3270 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3482 THR Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3851 PHE Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3914 LEU Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4077 ILE Chi-restraints excluded: chain A residue 4092 LEU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4234 GLN Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3868 SER Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 135 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 GLN B3247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107783 restraints weight = 24905.195| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.32 r_work: 0.3256 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17304 Z= 0.110 Angle : 0.457 14.962 23434 Z= 0.233 Chirality : 0.036 0.223 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.843 48.770 2357 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.13 % Allowed : 18.41 % Favored : 78.46 % 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 are not related in a simple way. whole: 2.79 (0.19), residues: 2146 helix: 2.84 (0.14), residues: 1447 sheet: 1.25 (0.64), residues: 72 loop : -0.54 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3228 TYR 0.013 0.001 TYR A4101 PHE 0.021 0.001 PHE A4108 TRP 0.007 0.001 TRP B3959 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00256 (17296) covalent geometry : angle 0.45523 (23422) hydrogen bonds : bond 0.03694 ( 1099) hydrogen bonds : angle 3.06976 ( 3258) metal coordination : bond 0.00399 ( 8) metal coordination : angle 1.81806 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.472 Fit side-chains REVERT: E 38 ARG cc_start: 0.7768 (tpp-160) cc_final: 0.7124 (ttm-80) REVERT: E 75 ARG cc_start: 0.7283 (mpp80) cc_final: 0.6830 (mpp80) REVERT: E 93 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: E 115 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7256 (pt0) REVERT: E 142 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6537 (t80) REVERT: E 146 MET cc_start: 0.6856 (mmt) cc_final: 0.6573 (mmp) REVERT: A 3228 ARG cc_start: 0.7853 (mtp85) cc_final: 0.6492 (ptt180) REVERT: A 3247 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: A 3310 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8798 (mt) REVERT: A 3537 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8228 (p0) REVERT: A 3871 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6849 (mptt) REVERT: A 4103 TRP cc_start: 0.7727 (t60) cc_final: 0.6860 (t-100) REVERT: A 4244 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8249 (tp) REVERT: C 303 GLU cc_start: 0.6646 (tm-30) cc_final: 0.5575 (tm-30) REVERT: B 3247 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: B 3504 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8689 (mt) REVERT: B 3523 ASP cc_start: 0.8160 (t0) cc_final: 0.7824 (t0) REVERT: B 3738 ASN cc_start: 0.8516 (t0) cc_final: 0.8203 (m110) REVERT: B 3774 LYS cc_start: 0.7524 (pttt) cc_final: 0.6416 (mmtt) REVERT: B 3851 PHE cc_start: 0.6139 (m-80) cc_final: 0.5790 (m-80) REVERT: B 3868 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.7191 (t) REVERT: B 3888 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8530 (ttp80) REVERT: B 3924 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: B 4091 GLU cc_start: 0.6101 (tp30) cc_final: 0.5567 (tp30) REVERT: B 4101 TYR cc_start: 0.7693 (m-80) cc_final: 0.7147 (m-10) REVERT: D 295 ARG cc_start: 0.7869 (mtt180) cc_final: 0.6698 (ptt180) outliers start: 57 outliers final: 44 residues processed: 210 average time/residue: 0.1263 time to fit residues: 39.6106 Evaluate side-chains 219 residues out of total 1951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3270 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3399 LEU Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3482 THR Chi-restraints excluded: chain A residue 3537 ASN Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3575 THR Chi-restraints excluded: chain A residue 3721 CYS Chi-restraints excluded: chain A residue 3762 ASN Chi-restraints excluded: chain A residue 3765 CYS Chi-restraints excluded: chain A residue 3851 PHE Chi-restraints excluded: chain A residue 3871 LYS Chi-restraints excluded: chain A residue 3914 LEU Chi-restraints excluded: chain A residue 3966 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4092 LEU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4234 GLN Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4278 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3259 SER Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3414 CYS Chi-restraints excluded: chain B residue 3504 LEU Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3611 ARG Chi-restraints excluded: chain B residue 3630 ASP Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3868 SER Chi-restraints excluded: chain B residue 3888 ARG Chi-restraints excluded: chain B residue 3924 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4155 ILE Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain D residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 161 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 159 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 GLN B3247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110417 restraints weight = 24981.110| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.29 r_work: 0.3272 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17304 Z= 0.096 Angle : 0.447 14.888 23434 Z= 0.228 Chirality : 0.035 0.220 2778 Planarity : 0.003 0.038 2959 Dihedral : 3.776 45.996 2357 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.02 % Allowed : 18.63 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.19), residues: 2146 helix: 2.87 (0.14), residues: 1451 sheet: 1.43 (0.65), residues: 70 loop : -0.52 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3228 TYR 0.013 0.001 TYR A4101 PHE 0.020 0.001 PHE A4108 TRP 0.005 0.001 TRP B3959 HIS 0.005 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00216 (17296) covalent geometry : angle 0.44555 (23422) hydrogen bonds : bond 0.03479 ( 1099) hydrogen bonds : angle 3.02436 ( 3258) metal coordination : bond 0.00358 ( 8) metal coordination : angle 1.70452 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.45 seconds wall clock time: 81 minutes 7.81 seconds (4867.81 seconds total)